Hello, I would like to ask for help about samtools mpileup. The output of samtools mpileup may differ depending on the presence or absence of the -f option. If there are probably about 20 bp deletions, some deletions are missing from the output.
$ samtools --version samtools 1.2 Using htslib 1.2.1 Copyright (C) 2015 Genome Research Ltd. $ samtools mpileup -r 1:943126-943126 in.bam 1 943126 N 27 c$c$ccccccccccccccccccccc-17nnnnnnnnnnnnnnnnnc-16nnnnnnnnnnnnnnnnc-24nnnnnnnnnnnnnnnnnnnnnnnnc-18nnnnnnnnnnnnnnnnnnc-17nnnnnnnnnnnnnnnnn CCCFF:B:IG6HJGGGGIBAEB00B5/ $ samtools mpileup -f GRCh37.fa -r 1:943126-943126 in.bam 1 943126 C 26 ,$,$,,,,,,,,,,,,,,,,,,,,,-17ttttttttttttttttt,-24tttttttttttttttttttttttt,-18tttttttttttttttttt,-17ttttttttttttttttt CCCFF:B:IG6HJGGGGIBAEB0B0/ I really hope you can help me. Thank you very much, Ken ------------------------------------------------------------------------------ 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
