Hi,
I am trying to call substitutions and indels in with samtools / bcftools
(versions 1.3.1 / 1.3.1-209-g1618245), and I am unable to call an indel that is
in the bam. Looking at the bam in a viewer confirms that there is an indel at
chr7 position 117559590 that deletes a TCT sequence. Following the instructions
on http://www.htslib.org/workflow/#mapping_to_variant, I used a similar
pipeline on the indexed bam:
samtools mpileup -x -d 1000000 -B -ugf <ref.fa> <sample.bam> | bcftools call
-vmO z -o <study.vcf.gz>
I added flags parameters -x, -d, -B because they seem relevant to this data,
and adding them do not seem to cause this issue I'm having.
Upon viewing the vcf, there does not appear to be any snp called at chr7
position 117559590:
...
"
chr7 117541810 . G T 11.4963 .
DP=1;SGB=-0.379885;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,0,1,0;MQ=40 GT:PL
0/1:39,3,0
chr7 117541812 . G T 10.5754 .
DP=1;SGB=-0.379885;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,0,1,0;MQ=40 GT:PL
0/1:38,3,0
chr7 117541813 . A G 11.4963 .
DP=1;SGB=-0.379885;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,0,1,0;MQ=40 GT:PL
0/1:39,3,0
chr7 117548628 . G T 210 .
DP=2032;VDB=0;SGB=-0.693147;RPB=0.925993;MQB=0;MQSB=0.9998;BQB=8.21384e-07;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=496,497,520,519;MQ=28
GT:PL 0/1:243,0,255
chr7 117559403 . A G 200 .
DP=344;VDB=0;SGB=-0.693147;RPB=0.995508;MQB=0.958341;BQB=0.736929;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=175,0,169,0;MQ=41
GT:PL
0/1:233,0,224
chr7 117559479 . G A 222 .
DP=694;VDB=0;SGB=-0.693147;RPB=6.85819e06;MQB=0.95608;MQSB=1;BQB=0.986478;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=180,179,167,168;MQ
=41 GT:PL 0/1:255,0,255
"
*** SHOULD BE HERE ***
"
chr7 117587989 . T C 11.4963 .
DP=1;SGB=-0.379885;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,0,0,1;MQ=40 GT:PL
0/1:39,3,0
chr7 117587995 . T A 11.4963 .
DP=1;SGB=-0.379885;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,0,0,1;MQ=40 GT:PL
0/1:39,3,0
chr7 117587997 . A G 11.4963 .
DP=1;SGB=-0.379885;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,0,0,1;MQ=40 GT:PL
0/1:39,3,0
chr7 117587999 . G T 11.4963 .
DP=1;SGB=-0.379885;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,0,0,1;MQ=40 GT:PL
0/1:39,3,0
"
...
I then used mpileup to generate a pileup file so I could confirm whether
mpileup was recognizing the snp. I used:
samtools mpileup -x -d 1000000 -B -f <ref.fa> -o <test.pileup> <sample.bam>
This yielded this output at the region of interest:
"
chr7 117559590 A 3686
.$..-3TCT..$.$.$.,-3tct,,-3tct,-3tct,,,,,,,,,-3tct,,,,,-3tct,-3tct,,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,-3tct,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,g,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,-3tct.-3TCT....-3TCT.-3TCT..-3TCT..-3TCT..-3TCT.-3TCT...-3TCT..-3TCT.-3TCT.....-3TCT......-3TCT.-3TCT.-3TCT..-3TCT..-3TCT..-3TCT..-3TCT.-3TCT.-3TCT.-3TCT..-3TCT..-3TCT....-3TCT....-3TCT.....-3TCT.-3TCT.....-3TCT...-3TCT..-3TCT.......-3TCT.-3TCT.-3TCT.-3TCT.-3TCT.-3TCT..-3TCT.-3TCT..-3TCT.-3TCT.-3TCT.-3TCT...-3TCT..-3TCT.....-3TCT.-3TCT.-3TCT.-3TCT.-3TCT...-3TCT.-3TCT.....-3TCT.-3TCT...-3TCT...-3TCT..-3TCT.-3TCT.-3TCT.-3TCT...-3TCT...-3TCT..-3TCT.-3TCT.-3TCT.-3TCT..-3TCT..-3TCT...-3TCT.......-3TCT...-3TCT.....-3TCT......-3TCT.-3TCT.....-3TCT.-3TCT..-3TCT.-3TCT...-3TCT..-3TCT..-3TCT......-3TCT.-3TCT.-3TCT.-3TCT.-3TCT...-3TCT..-3TCT.-3TCT..-3TCT.-3TCT..-3TCT.-3TCT.-3TCT.-3TCT...-3TCT..-3TCT.-3TCT..-3TCT..-3TCT.-3TCT.-3TCT.-3TCT..-3TCT.
"
...
"
HHHHH<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
"
This pileup data is consistent with the bam viewer I used, yet somehow there is
a disconnect in calling the indel in the final vcf. Hopefully I'm just missing
a flag or parameter. Any thoughts on why I am not able to call this snp? Any
help will be greatly appreciated!
Thanks,
-dylan
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Samtools-help mailing list
Samtools-help@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/samtools-help
