I can provide a bit more details to my question. I've managed to create bam input that gives rise to the following mpileup output:
[snip] chrX 8982279 g 10 .......... EJIJJJJC;J chrX 8982280 a 10 .......... DHJJJJJ@HJ chrX 8982281 a 10 .......... DHHJJJJIBI chrX 8982282 a 10 .......... DHHHJJJIEJ chrX 8982283 a 10 .......... DHHGHJJHEJ chrX 8982284 a 10 .......... DHHHHHJHIJ chrX 8982285 c 10 .......... DFHHHHHFIJ chrX 8982286 g 10 .......... DFFHHHGCGJ chrX 8982287 c 10 .......... DFFFHHH:HJ chrX 8982288 a 10 .......... DFFFFHHDBH chrX 8982289 g 10 .......... DFFFFFHFDH chrX 8982290 a 10 .-1241CAACGTAAGATTTAAAACATGACTCGTTGCGAACCTCGATCAATGTCGGCTGCGCGATTTTTTCAAAGCTTATTATTTGATACTCACTATCAGGAAAGCAGTACGCAGGAAAGCAACACATTATGAAAATATTTAGAAAATGAGATTTGTGATTGAACCACATAAAACATTCAATTTCATAAACATAAATTATTTATTAAACTATCAACGTACAACAGCAATAACATTTTTGAAGATTGGAACTATAATTGGCTTTACTTGGATTTTCTCTATCCTTTGTGCTATGCCCTTTGCGATCCATCACCGAGCCGATTACATTATGAAAAGCTGGCCAGGGACAGACAACAGAATACCGGTAAAATAGAGTTTATTGACAATAACTCAGCAAAGTCTTTTAAGGTTAAATCTTCAAAAATGTGCATGATAGCAGTGATGTTTGAACCAAAGCTAGCGTCAACTTTTAAGGTAGTTAATAAATAAAAATTATCTTATACAGGGTGCAAGTTTGTATATTTTTTTCAGATTCTATTTCACTTCTCTGCCATAGCATTCTTTGCACTCCCACTGTTTACAATTGTAATTCTCTATGCAAGAATTGCATGTAAGGTAAGAAAAGTTGAACGGTGAAAAGCAAATTTTAAATTCACATTAAAACATTGATTGTTTTAAAATGAACGTTTTAATATCGTAATGAATAACGGATACACGTAAAACAAAAATTAAACAAAAACTCACCTGTTCTTTCATTTAGGTATCCAGCAACAGAACAATTCAACCAGGCGAACTTGATATCACTGAGGAACTGCAAATGAGAATCAATGCAATTTTATGTGAGTTCGGGATGAGTTGTTGATAAAAAACAGATGTAGGAGGGGTAGAAAATTGGAAAGTGAGGAACCGAATATGGGAGGGATTGGAGCGGAAAACGAATGCGTGAGCAGAGACTAGAAATGGATGTACTTAGATGAAGTACAAACTATCGTATTGTTCCA TACAATTT TCAGTGGATATTTTTGTATTTTTCGGAATTTCGAGAACTGCGGTAGTTTATTGTTTAGTAACAGAGTTTTTAGTAACAAAGAGTAGAAACAAGGTAAAGTGACAATTTATGCAAATTTTGGGTTTTCTGGATGAATACTGTTTTTCACTTTAACTGTTATATTTTGTCACTACAGATAAAATATTGTATGTTCCCAAAAAGTGAGAAAAATATGAGCACATTTTGTCATTGTCTAGTGGCG.-1241CAACGTAAGATTTAAAACATGACTCGTTGCGAACCTCGATCAATGTCGGCTGCGCGATTTTTTCAAAGCTTATTATTTGATACTCACTATCAGGAAAGCAGTACGCAGGAAAGCAACACATTATGAAAATATTTAGAAAATGAGATTTGTGATTGAACCACATAAAACATTCAATTTCATAAACATAAATTATTTATTAAACTATCAACGTACAACAGCAATAACATTTTTGAAGATTGGAACTATAATTGGCTTTACTTGGATTTTCTCTATCCTTTGTGCTATGCCCTTTGCGATCCATCACCGAGCCGATTACATTATGAAAAGCTGGCCAGGGACAGACAACAGAATACCGGTAAAATAGAGTTTATTGACAATAACTCAGCAAAGTCTTTTAAGGTTAAATCTTCAAAAATGTGCATGATAGCAGTGATGTTTGAACCAAAGCTAGCGTCAACTTTTAAGGTAGTTAATAAATAAAAATTATCTTATACAGGGTGCAAGTTTGTATATTTTTTTCAGATTCTATTTCACTTCTCTGCCATAGCATTCTTTGCACTCCCACTGTTTACAATTGTAATTCTCTATGCAAGAATTGCATGTAAGGTAAGAAAAGTTGAACGGTGAAAAGCAAATTTTAAATTCACATTAAAACATTGATTGTTTTAAAATGAACGTTTTAATATCGTAATGAATAACGGATACACGTAAAACAAAAATTAAACAAAAACTCACCTGTTCTTTCATTTAG GTATCCAGCAACAGAACAATTCAACC AGGCGAACTTGATATCACTGAGGAACTGCAAATGAGAATCAATGCAATTTTATGTGAGTTCGGGATGAGTTGTTGATAAAAAACAGATGTAGGAGGGGTAGAAAATTGGAAAGTGAGGAACCGAATATGGGAGGGATTGGAGCGGAAAACGAATGCGTGAGCAGAGACTAGAAATGGATGTACTTAGATGAAGTACAAACTATCGTATTGTTCCATACAATTTTCAGTGGATATTTTTGTATTTTTCGGAATTTCGAGAACTGCGGTAGTTTATTGTTTAGTAACAGAGTTTTTAGTAACAAAGAGTAGAAACAAGGTAAAGTGACAATTTATGCAAATTTTGGGTTTTCTGGATGAATACTGTTTTTCACTTTAACTGTTATATTTTGTCACTACAGATAAAATATTGTATGTTCCCAAAAAGTGAGAAAAATATGAGCACATTTTGTCATTGTCTAGTGGCG.-1241CAACGTAAGATTTAAAACATGACTCGTTGCGAACCTCGATCAATGTCGGCTGCGCGATTTTTTCAAAGCTTATTATTTGATACTCACTATCAGGAAAGCAGTACGCAGGAAAGCAACACATTATGAAAATATTTAGAAAATGAGATTTGTGATTGAACCACATAAAACATTCAATTTCATAAACATAAATTATTTATTAAACTATCAACGTACAACAGCAATAACATTTTTGAAGATTGGAACTATAATTGGCTTTACTTGGATTTTCTCTATCCTTTGTGCTATGCCCTTTGCGATCCATCACCGAGCCGATTACATTATGAAAAGCTGGCCAGGGACAGACAACAGAATACCGGTAAAATAGAGTTTATTGACAATAACTCAGCAAAGTCTTTTAAGGTTAAATCTTCAAAAATGTGCATGATAGCAGTGATGTTTGAACCAAAGCTAGCGTCAACTTTTAAGGTAGTTAATAAATAAAAATTATCTTATACAGGGTGCAAGTTTGTATATTTTTTTCAGATTCTA TTTCACTTCTCTGCCATAGCATTCTT TGCACTCCCACTGTTTACAATTGTAATTCTCTATGCAAGAATTGCATGTAAGGTAAGAAAAGTTGAACGGTGAAAAGCAAATTTTAAATTCACATTAAAACATTGATTGTTTTAAAATGAACGTTTTAATATCGTAATGAATAACGGATACACGTAAAACAAAAATTAAACAAAAACTCACCTGTTCTTTCATTTAGGTATCCAGCAACAGAACAATTCAACCAGGCGAACTTGATATCACTGAGGAACTGCAAATGAGAATCAATGCAATTTTATGTGAGTTCGGGATGAGTTGTTGATAAAAAACAGATGTAGGAGGGGTAGAAAATTGGAAAGTGAGGAACCGAATATGGGAGGGATTGGAGCGGAAAACGAATGCGTGAGCAGAGACTAGAAATGGATGTACTTAGATGAAGTACAAACTATCGTATTGTTCCATACAATTTTCAGTGGATATTTTTGTATTTTTCGGAATTTCGAGAACTGCGGTAGTTTATTGTTTAGTAACAGAGTTTTTAGTAACAAAGAGTAGAAACAAGGTAAAGTGACAATTTATGCAAATTTTGGGTTTTCTGGATGAATACTGTTTTTCACTTTAACTGTTATATTTTGTCACTACAGATAAAATATTGTATGTTCCCAAAAAGTGAGAAAAATATGAGCACATTTTGTCATTGTCTAGTGGCG.-1241CAACGTAAGATTTAAAACATGACTCGTTGCGAACCTCGATCAATGTCGGCTGCGCGATTTTTTCAAAGCTTATTATTTGATACTCACTATCAGGAAAGCAGTACGCAGGAAAGCAACACATTATGAAAATATTTAGAAAATGAGATTTGTGATTGAACCACATAAAACATTCAATTTCATAAACATAAATTATTTATTAAACTATCAACGTACAACAGCAATAACATTTTTGAAGATTGGAACTATAATTGGCTTTACTTGGATTTTCTCTATCCTTTGTGCTATGCCCTTTGCGATCCATCACC GAGCCGATTACATTATGAAAAGCTGG CCAGGGACAGACAACAGAATACCGGTAAAATAGAGTTTATTGACAATAACTCAGCAAAGTCTTTTAAGGTTAAATCTTCAAAAATGTGCATGATAGCAGTGATGTTTGAACCAAAGCTAGCGTCAACTTTTAAGGTAGTTAATAAATAAAAATTATCTTATACAGGGTGCAAGTTTGTATATTTTTTTCAGATTCTATTTCACTTCTCTGCCATAGCATTCTTTGCACTCCCACTGTTTACAATTGTAATTCTCTATGCAAGAATTGCATGTAAGGTAAGAAAAGTTGAACGGTGAAAAGCAAATTTTAAATTCACATTAAAACATTGATTGTTTTAAAATGAACGTTTTAATATCGTAATGAATAACGGATACACGTAAAACAAAAATTAAACAAAAACTCACCTGTTCTTTCATTTAGGTATCCAGCAACAGAACAATTCAACCAGGCGAACTTGATATCACTGAGGAACTGCAAATGAGAATCAATGCAATTTTATGTGAGTTCGGGATGAGTTGTTGATAAAAAACAGATGTAGGAGGGGTAGAAAATTGGAAAGTGAGGAACCGAATATGGGAGGGATTGGAGCGGAAAACGAATGCGTGAGCAGAGACTAGAAATGGATGTACTTAGATGAAGTACAAACTATCGTATTGTTCCATACAATTTTCAGTGGATATTTTTGTATTTTTCGGAATTTCGAGAACTGCGGTAGTTTATTGTTTAGTAACAGAGTTTTTAGTAACAAAGAGTAGAAACAAGGTAAAGTGACAATTTATGCAAATTTTGGGTTTTCTGGATGAATACTGTTTTTCACTTTAACTGTTATATTTTGTCACTACAGATAAAATATTGTATGTTCCCAAAAAGTGAGAAAAATATGAGCACATTTTGTCATTGTCTAGTGGCG.-1241CAACGTAAGATTTAAAACATGACTCGTTGCGAACCTCGATCAATGTCGGCTGCGCGATTTTTTCAAAGCTTATTATTTGATA CTCACTATCAGGAAAGCAGTACGCAG GAAAGCAACACATTATGAAAATATTTAGAAAATGAGATTTGTGATTGAACCACATAAAACATTCAATTTCATAAACATAAATTATTTATTAAACTATCAACGTACAACAGCAATAACATTTTTGAAGATTGGAACTATAATTGGCTTTACTTGGATTTTCTCTATCCTTTGTGCTATGCCCTTTGCGATCCATCACCGAGCCGATTACATTATGAAAAGCTGGCCAGGGACAGACAACAGAATACCGGTAAAATAGAGTTTATTGACAATAACTCAGCAAAGTCTTTTAAGGTTAAATCTTCAAAAATGTGCATGATAGCAGTGATGTTTGAACCAAAGCTAGCGTCAACTTTTAAGGTAGTTAATAAATAAAAATTATCTTATACAGGGTGCAAGTTTGTATATTTTTTTCAGATTCTATTTCACTTCTCTGCCATAGCATTCTTTGCACTCCCACTGTTTACAATTGTAATTCTCTATGCAAGAATTGCATGTAAGGTAAGAAAAGTTGAACGGTGAAAAGCAAATTTTAAATTCACATTAAAACATTGATTGTTTTAAAATGAACGTTTTAATATCGTAATGAATAACGGATACACGTAAAACAAAAATTAAACAAAAACTCACCTGTTCTTTCATTTAGGTATCCAGCAACAGAACAATTCAACCAGGCGAACTTGATATCACTGAGGAACTGCAAATGAGAATCAATGCAATTTTATGTGAGTTCGGGATGAGTTGTTGATAAAAAACAGATGTAGGAGGGGTAGAAAATTGGAAAGTGAGGAACCGAATATGGGAGGGATTGGAGCGGAAAACGAATGCGTGAGCAGAGACTAGAAATGGATGTACTTAGATGAAGTACAAACTATCGTATTGTTCCATACAATTTTCAGTGGATATTTTTGTATTTTTCGGAATTTCGAGAACTGCGGTAGTTTATTGTTTAGTAACAGAGTTTTTAGTAACAAAGAGTAGAAACAAGGTAAAGTGACAAT TTATGCAAATTTTGGGTTTTCTGGAT GAATACTGTTTTTCACTTTAACTGTTATATTTTGTCACTACAGATAAAATATTGTATGTTCCCAAAAAGTGAGAAAAATATGAGCACATTTTGTCATTGTCTAGTGGCG.-1241CAACGTAAGATTTAAAACATGACTCGTTGCGAACCTCGATCAATGTCGGCTGCGCGATTTTTTCAAAGCTTATTATTTGATACTCACTATCAGGAAAGCAGTACGCAGGAAAGCAACACATTATGAAAATATTTAGAAAATGAGATTTGTGATTGAACCACATAAAACATTCAATTTCATAAACATAAATTATTTATTAAACTATCAACGTACAACAGCAATAACATTTTTGAAGATTGGAACTATAATTGGCTTTACTTGGATTTTCTCTATCCTTTGTGCTATGCCCTTTGCGATCCATCACCGAGCCGATTACATTATGAAAAGCTGGCCAGGGACAGACAACAGAATACCGGTAAAATAGAGTTTATTGACAATAACTCAGCAAAGTCTTTTAAGGTTAAATCTTCAAAAATGTGCATGATAGCAGTGATGTTTGAACCAAAGCTAGCGTCAACTTTTAAGGTAGTTAATAAATAAAAATTATCTTATACAGGGTGCAAGTTTGTATATTTTTTTCAGATTCTATTTCACTTCTCTGCCATAGCATTCTTTGCACTCCCACTGTTTACAATTGTAATTCTCTATGCAAGAATTGCATGTAAGGTAAGAAAAGTTGAACGGTGAAAAGCAAATTTTAAATTCACATTAAAACATTGATTGTTTTAAAATGAACGTTTTAATATCGTAATGAATAACGGATACACGTAAAACAAAAATTAAACAAAAACTCACCTGTTCTTTCATTTAGGTATCCAGCAACAGAACAATTCAACCAGGCGAACTTGATATCACTGAGGAACTGCAAATGAGAATCAATGCAATTTTATGTGAGTTCGGGATGAGTTGTTGATAAAAAACAGATGTAGGAGGGGTAGAAAAT TGGAAAGTGAGGAACCGAATATGGGA GGGATTGGAGCGGAAAACGAATGCGTGAGCAGAGACTAGAAATGGATGTACTTAGATGAAGTACAAACTATCGTATTGTTCCATACAATTTTCAGTGGATATTTTTGTATTTTTCGGAATTTCGAGAACTGCGGTAGTTTATTGTTTAGTAACAGAGTTTTTAGTAACAAAGAGTAGAAACAAGGTAAAGTGACAATTTATGCAAATTTTGGGTTTTCTGGATGAATACTGTTTTTCACTTTAACTGTTATATTTTGTCACTACAGATAAAATATTGTATGTTCCCAAAAAGTGAGAAAAATATGAGCACATTTTGTCATTGTCTAGTGGCG.-1241CAACGTAAGATTTAAAACATGACTCGTTGCGAACCTCGATCAATGTCGGCTGCGCGATTTTTTCAAAGCTTATTATTTGATACTCACTATCAGGAAAGCAGTACGCAGGAAAGCAACACATTATGAAAATATTTAGAAAATGAGATTTGTGATTGAACCACATAAAACATTCAATTTCATAAACATAAATTATTTATTAAACTATCAACGTACAACAGCAATAACATTTTTGAAGATTGGAACTATAATTGGCTTTACTTGGATTTTCTCTATCCTTTGTGCTATGCCCTTTGCGATCCATCACCGAGCCGATTACATTATGAAAAGCTGGCCAGGGACAGACAACAGAATACCGGTAAAATAGAGTTTATTGACAATAACTCAGCAAAGTCTTTTAAGGTTAAATCTTCAAAAATGTGCATGATAGCAGTGATGTTTGAACCAAAGCTAGCGTCAACTTTTAAGGTAGTTAATAAATAAAAATTATCTTATACAGGGTGCAAGTTTGTATATTTTTTTCAGATTCTATTTCACTTCTCTGCCATAGCATTCTTTGCACTCCCACTGTTTACAATTGTAATTCTCTATGCAAGAATTGCATGTAAGGTAAGAAAAGTTGAACGGTGAAAAGCAAATTTTAAATTCACATTAAAACATTGA TTGTTTTAAAATGAACGTTTTAATAT CGTAATGAATAACGGATACACGTAAAACAAAAATTAAACAAAAACTCACCTGTTCTTTCATTTAGGTATCCAGCAACAGAACAATTCAACCAGGCGAACTTGATATCACTGAGGAACTGCAAATGAGAATCAATGCAATTTTATGTGAGTTCGGGATGAGTTGTTGATAAAAAACAGATGTAGGAGGGGTAGAAAATTGGAAAGTGAGGAACCGAATATGGGAGGGATTGGAGCGGAAAACGAATGCGTGAGCAGAGACTAGAAATGGATGTACTTAGATGAAGTACAAACTATCGTATTGTTCCATACAATTTTCAGTGGATATTTTTGTATTTTTCGGAATTTCGAGAACTGCGGTAGTTTATTGTTTAGTAACAGAGTTTTTAGTAACAAAGAGTAGAAACAAGGTAAAGTGACAATTTATGCAAATTTTGGGTTTTCTGGATGAATACTGTTTTTCACTTTAACTGTTATATTTTGTCACTACAGATAAAATATTGTATGTTCCCAAAAAGTGAGAAAAATATGAGCACATTTTGTCATTGTCTAGTGGCG.-1241CAACGTAAGATTTAAAACATGACTCGTTGCGAACCTCGATCAATGTCGGCTGCGCGATTTTTTCAAAGCTTATTATTTGATACTCACTATCAGGAAAGCAGTACGCAGGAAAGCAACACATTATGAAAATATTTAGAAAATGAGATTTGTGATTGAACCACATAAAACATTCAATTTCATAAACATAAATTATTTATTAAACTATCAACGTACAACAGCAATAACATTTTTGAAGATTGGAACTATAATTGGCTTTACTTGGATTTTCTCTATCCTTTGTGCTATGCCCTTTGCGATCCATCACCGAGCCGATTACATTATGAAAAGCTGGCCAGGGACAGACAACAGAATACCGGTAAAATAGAGTTTATTGACAATAACTCAGCAAAGTCTTTTAAGGTTAAATCTTCAAAAATGTGCATGATAGCAGTGATGTT TGAACCAAAGCTAGCGTCAACTTTTA AGGTAGTTAATAAATAAAAATTATCTTATACAGGGTGCAAGTTTGTATATTTTTTTCAGATTCTATTTCACTTCTCTGCCATAGCATTCTTTGCACTCCCACTGTTTACAATTGTAATTCTCTATGCAAGAATTGCATGTAAGGTAAGAAAAGTTGAACGGTGAAAAGCAAATTTTAAATTCACATTAAAACATTGATTGTTTTAAAATGAACGTTTTAATATCGTAATGAATAACGGATACACGTAAAACAAAAATTAAACAAAAACTCACCTGTTCTTTCATTTAGGTATCCAGCAACAGAACAATTCAACCAGGCGAACTTGATATCACTGAGGAACTGCAAATGAGAATCAATGCAATTTTATGTGAGTTCGGGATGAGTTGTTGATAAAAAACAGATGTAGGAGGGGTAGAAAATTGGAAAGTGAGGAACCGAATATGGGAGGGATTGGAGCGGAAAACGAATGCGTGAGCAGAGACTAGAAATGGATGTACTTAGATGAAGTACAAACTATCGTATTGTTCCATACAATTTTCAGTGGATATTTTTGTATTTTTCGGAATTTCGAGAACTGCGGTAGTTTATTGTTTAGTAACAGAGTTTTTAGTAACAAAGAGTAGAAACAAGGTAAAGTGACAATTTATGCAAATTTTGGGTTTTCTGGATGAATACTGTTTTTCACTTTAACTGTTATATTTTGTCACTACAGATAAAATATTGTATGTTCCCAAAAAGTGAGAAAAATATGAGCACATTTTGTCATTGTCTAGTGGCG.-1241CAACGTAAGATTTAAAACATGACTCGTTGCGAACCTCGATCAATGTCGGCTGCGCGATTTTTTCAAAGCTTATTATTTGATACTCACTATCAGGAAAGCAGTACGCAGGAAAGCAACACATTATGAAAATATTTAGAAAATGAGATTTGTGATTGAACCACATAAAACATTCAATTTCATAAACATAAATTATTTATTAAACTATCAACGTACA ACAGCAATAACATTTTTGAAGATTGG AACTATAATTGGCTTTACTTGGATTTTCTCTATCCTTTGTGCTATGCCCTTTGCGATCCATCACCGAGCCGATTACATTATGAAAAGCTGGCCAGGGACAGACAACAGAATACCGGTAAAATAGAGTTTATTGACAATAACTCAGCAAAGTCTTTTAAGGTTAAATCTTCAAAAATGTGCATGATAGCAGTGATGTTTGAACCAAAGCTAGCGTCAACTTTTAAGGTAGTTAATAAATAAAAATTATCTTATACAGGGTGCAAGTTTGTATATTTTTTTCAGATTCTATTTCACTTCTCTGCCATAGCATTCTTTGCACTCCCACTGTTTACAATTGTAATTCTCTATGCAAGAATTGCATGTAAGGTAAGAAAAGTTGAACGGTGAAAAGCAAATTTTAAATTCACATTAAAACATTGATTGTTTTAAAATGAACGTTTTAATATCGTAATGAATAACGGATACACGTAAAACAAAAATTAAACAAAAACTCACCTGTTCTTTCATTTAGGTATCCAGCAACAGAACAATTCAACCAGGCGAACTTGATATCACTGAGGAACTGCAAATGAGAATCAATGCAATTTTATGTGAGTTCGGGATGAGTTGTTGATAAAAAACAGATGTAGGAGGGGTAGAAAATTGGAAAGTGAGGAACCGAATATGGGAGGGATTGGAGCGGAAAACGAATGCGTGAGCAGAGACTAGAAATGGATGTACTTAGATGAAGTACAAACTATCGTATTGTTCCATACAATTTTCAGTGGATATTTTTGTATTTTTCGGAATTTCGAGAACTGCGGTAGTTTATTGTTTAGTAACAGAGTTTTTAGTAACAAAGAGTAGAAACAAGGTAAAGTGACAATTTATGCAAATTTTGGGTTTTCTGGATGAATACTGTTTTTCACTTTAACTGTTATATTTTGTCACTACAGATAAAATATTGTATGTTCCCAAAAAGTGAGAAAAATATGAGCACATTTTGTCATTGTCTAGTG GCG.- 1241CAACGTAAGATTTAAAACATGACTCGTTGCGAACCTCGATCAATGTCGGCTGCGCGATTTTTTCAAAGCTTATTATTTGATACTCACTATCAGGAAAGCAGTACGCAGGAAAGCAACACATTATGAAAATATTTAGAAAATGAGATTTGTGATTGAACCACATAAAACATTCAATTTCATAAACATAAATTATTTATTAAACTATCAACGTACAACAGCAATAACATTTTTGAAGATTGGAACTATAATTGGCTTTACTTGGATTTTCTCTATCCTTTGTGCTATGCCCTTTGCGATCCATCACCGAGCCGATTACATTATGAAAAGCTGGCCAGGGACAGACAACAGAATACCGGTAAAATAGAGTTTATTGACAATAACTCAGCAAAGTCTTTTAAGGTTAAATCTTCAAAAATGTGCATGATAGCAGTGATGTTTGAACCAAAGCTAGCGTCAACTTTTAAGGTAGTTAATAAATAAAAATTATCTTATACAGGGTGCAAGTTTGTATATTTTTTTCAGATTCTATTTCACTTCTCTGCCATAGCATTCTTTGCACTCCCACTGTTTACAATTGTAATTCTCTATGCAAGAATTGCATGTAAGGTAAGAAAAGTTGAACGGTGAAAAGCAAATTTTAAATTCACATTAAAACATTGATTGTTTTAAAATGAACGTTTTAATATCGTAATGAATAACGGATACACGTAAAACAAAAATTAAACAAAAACTCACCTGTTCTTTCATTTAGGTATCCAGCAACAGAACAATTCAACCAGGCGAACTTGATATCACTGAGGAACTGCAAATGAGAATCAATGCAATTTTATGTGAGTTCGGGATGAGTTGTTGATAAAAAACAGATGTAGGAGGGGTAGAAAATTGGAAAGTGAGGAACCGAATATGGGAGGGATTGGAGCGGAAAACGAATGCGTGAGCAGAGACTAGAAATGGATGTACTTAGATGAAGTACAAACTATCGTATTGTTCCATA CAATTTTCAGTGGATATTTTTGTATT TTTCGGAATTTCGAGAACTGCGGTAGTTTATTGTTTAGTAACAGAGTTTTTAGTAACAAAGAGTAGAAACAAGGTAAAGTGACAATTTATGCAAATTTTGGGTTTTCTGGATGAATACTGTTTTTCACTTTAACTGTTATATTTTGTCACTACAGATAAAATATTGTATGTTCCCAAAAAGTGAGAAAAATATGAGCACATTTTGTCATTGTCTAGTGGCG DCFFFFFHHH chrX 8982291 c 10 ********** DCCFFFFDDH chrX 8982292 a 10 ********** DCCFFFFDDH chrX 8982293 a 10 ********** DCCFFFFDDH chrX 8982294 c 10 ********** DCCFFFFDDH chrX 8982295 g 10 ********** DCCFFFFDDH chrX 8982296 t 10 ********** DCCFFFFDDH chrX 8982297 a 10 ********** DCCFFFFDDH chrX 8982298 a 10 ********** DCCFFFFDDH chrX 8982299 g 10 ********** DCCFFFFDDH chrX 8982300 a 10 ********** DCCFFFFDDH chrX 8982301 t 10 ********** DCCFFFFDDH chrX 8982302 t 10 ********** DCCFFFFDDH chrX 8982303 t 10 ********** DCCFFFFDDH chrX 8982304 a 10 ********** DCCFFFFDDH chrX 8982305 a 10 ********** DCCFFFFDDH chrX 8982306 a 10 ********** DCCFFFFDDH chrX 8982307 a 10 ********** DCCFFFFDDH chrX 8982308 c 10 ********** DCCFFFFDDH chrX 8982309 a 10 ********** DCCFFFFDDH chrX 8982310 t 10 ********** DCCFFFFDDH chrX 8982311 g 10 ********** DCCFFFFDDH chrX 8982312 a 10 ********** DCCFFFFDDH chrX 8982313 c 10 ********** DCCFFFFDDH chrX 8982314 t 10 ********** DCCFFFFDDH chrX 8982315 c 10 ********** DCCFFFFDDH chrX 8982316 g 10 ********** DCCFFFFDDH chrX 8982317 t 10 ********** DCCFFFFDDH chrX 8982318 t 10 ********** DCCFFFFDDH chrX 8982319 g 10 ********** DCCFFFFDDH chrX 8982320 c 10 ********** DCCFFFFDDH chrX 8982321 g 10 ********** DCCFFFFDDH chrX 8982322 a 10 ********** DCCFFFFDDH chrX 8982323 a 10 ********** DCCFFFFDDH chrX 8982324 c 10 ********** DCCFFFFDDH chrX 8982325 c 10 ********** DCCFFFFDDH chrX 8982326 t 10 ********** DCCFFFFDDH chrX 8982327 c 10 ********** DCCFFFFDDH chrX 8982328 g 10 ********** DCCFFFFDDH chrX 8982329 a 10 ********** DCCFFFFDDH chrX 8982330 t 10 ********** DCCFFFFDDH chrX 8982331 c 10 ********** DCCFFFFDDH chrX 8982332 a 10 ********** DCCFFFFDDH [/snip] indicating a 1241bp deletion on chrX (actually, this is C.elegans data). However, when I do genotype calling on the same bam input using samtools mpileup -r chrX:8900000-9000000 -Dgu -f WS220.64_chr.fa input.bam | bcftools view -gv - > output.vcf then that deletion is totally ignored (I tried already - with no effect - disabling BAQ calculation and -Q 0 just to make sure those aren't the problem). I am just looking for an explanation for this behavior and, ideally, a solution that allows me to keep using samtools for aligned input like this. The thought behind this is that I would like to stick with one variant caller for everything (SNVs, indels, deletions) instead of invoking different ones for every variant type. Any thoughts? Wolfgang Wolfgang Maier <wolfgang.maier <at> biologie.uni-freiburg.de> writes: > > I'm currently experimenting with split-reads alignment to detect > deletions in WGS data and I'm wondering whether samtools mpileup > combined with bcftools is able to call larger deletions (typically > several hundred bases) as opposed to just small indels when presented > with appropriately aligned reads. > From a first test with samtools 0.1.19 and engineered bam data > simulating a 1.4 kb deletion the answer seems to be no, but I'd be > grateful for any help or explanation why it can't work. > > Thanks a lot, > Wolfgang > ------------------------------------------------------------------------------ Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. 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