Hi, I just discovered that the dinucleotide deletion is present in standard 'mpileup output' format, but is missing if I use the -v flag to convert to vcf during the mpileup run. I'm pasting the mpileup output below.
I need vcf and I need it to contain the indels. I'm wondering if there is a reason for this I'm not aware of and/or knows how to capture indels from mpileup output into vcf format? Best, Jonathan $samtools mpileup -AB -d10000 -l positionList -f $ref littleBam2.bam [mpileup] 1 samples in 1 input files 10 8111431 C 291 ..,............,..,,..,,,.....,................,,,,.....................,,..........,,,.......,,...,,,,,.....,,,..,,,................,...,...,,,,,,...,..........,,....,.........,,,...,,.......................,,.....,.......,....,..,,,......,.......................,,.....,...,,,.....,.,,^].^].^].^]. <@A8=..>8>;?@8>:@.1A>@=AA@@?@@>@@@@@@@@@@;@@?@@7AAA@@@@=@@@@@@@@@=@@?=@@@A@ @@@@@@@@@>AA@@@@@@@AA?@@AAAAA@@@@@AAA@@AAA??6??=?@8@ @@@@@@A???A?998A>A>A???A@ ?@@@????@A>@?@@A??@@?@@@?;9>??=>A????@?@@;????@@?@@??@@?A8@@@?@A@@@?@?@A@ ???A@?AAA??@??@>@???@@@?@??@@??@@@@<;@?AA@?<@@?AAA;AA???>>?@@@?AA? 10 8111432 T 294 .$.,............C,..,,..,,,.....,...............-2CA.,,,,,.....-2CA................,,..........,,,.......,,...,,,,,.....,,,..,,,................,...,...,,,,,,...,..........,,....,.........-2CA,,,...,,.......................,,.....,.......,..-2CA..,..,,,......,.....-2CA..................,,.....,..-2CA.,,.....,.,,....^].^]?A@ ??.6A@;9=A?A.;A.?@;A?@@AAAAA@AAAAAAAAAA ;AAAA8?@??=AAAAAAAAAAA8AAAAAAAAA>@AAAAAAAA@A=@?AAAAAAA@@AAA@@@@@AAAAA@@@AA@ @@A?;@@;@@>AAAA@AA=@@@@@@@@@@@7@@@@@A@@@@@@@@@@@A>AA@@@AA@AAA @.@>@@@=@@@@>:@AA?@@@@AA@AA@@AA@@@AAA@A@AAA@?@A@A@@<@A@@@@@@A@@A@A@@@AAA@A8 @AA@@AAAA@?A>@@A@AAA@AAA@=A@@@@<@:>?AA??? 10 8111433 C 294 .,..........,..,,..,,,.....,..............*.,,,,,....*................,,..........,,,.......,,...,,,,,.....,,,..,,,................,...,...,,,,,,...,..........,,....,........*,,,...,,.......................,.....,.......,.*..,..,,,......,....*..................,,.....,.*.,,,.....,.,,......^].^],^],^], @A=@8.:>88@@6?.7>>>@>>@@@@@2>@@@@@@@=@@@@@[email protected]. @@@@=@@@@@@@@@=@@@@@@8?@@@@@@@@@@>7>@@@@>@@>A@@@AA>A.@@@@@A@A@@>AA@ ??????79????@?@=@@@A???=AAAAA???A9?????????8A????A=?@@?@@@@7A;???.A???=@?@@>????@@?@@??@@?8@ @@?@@@@@?@?@A@@??A@?@=A??@??@A@???A@@?@:?@@??@@@@?@@?AA@?@@@A@A @AAA?@@??@A??>>?>=>???? On Sat, Aug 22, 2015 at 5:35 PM, Jo R <[email protected]> wrote: > > littleBam1.bam > <https://drive.google.com/file/d/0Bygo_633ok9Vd21WZkxTTC0tTjg/view?usp=drive_web> > > littleBam2.bam > <https://drive.google.com/file/d/0Bygo_633ok9VM2VmOWtyR2gya2c/view?usp=drive_web> > > positionList > <https://drive.google.com/file/d/0Bygo_633ok9Vbm1jMnROcGZVN0U/view?usp=drive_web> > Hello, > I'm attempting to genotype certain positions across several bam files. > > I have two bam files with the same deletion. Oddly, mpileup picks it up > perfectly from the first bam, but totally misses it in the second. I can't > figure out why. > > I'm attaching a small piece of each of the two bam files, and the file > containing the positions, in case there is someone out there willing and > able to help troubleshoot. > > I'm using Samtools (HTSlib) v. 1.2 > > The first bam file: > > $samtools mpileup -AvuB -d10000 -l positionList -f $ref littleBam1.bam > > > #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT > s_Hyman_01_9 > 10 8111431 . C <X> 0 . > DP=242;I16=187,54,0,0,7379,228331,0,0,14217,845755,0,0,4591,103019,0,0;QS=1,0;MQSB=0.827163;MQ0F=0 > PL 0,255,255 > 10 8111432 . T <X> 0 . > DP=245;I16=189,53,0,0,7411,229565,0,0,14318,852594,0,0,4605,103407,0,0;QS=1,0;MQSB=0.783638;MQ0F=0 > PL 0,255,255 > 10 8111432 . TCA T 0 . > INDEL;IDV=7;IMF=0.0285714;DP=245;I16=180,51,5,2,14448,925348,360,18982,13751,821999,420,25200,4400,98888,139,3165;QS=0.973292,0.0267082;VDB=0.0104629;SGB=-0.636426;MQSB=0.771887;MQ0F=0 > PL 0,255,255 > 10 8111433 . C <X> 0 . > DP=242;I16=186,51,0,0,7253,224967,0,0,14032,836174,0,0,4476,100386,0,0;QS=1,0;MQSB=0.850882;MQ0F=0 > PL 0,255,255 > -bash-4.1$ > > > There it is! At position 8111432. > > > From the second bam file: > > > $samtools mpileup -AvuB -d10000 -l positionList -f $ref littleBam2.bam > > > #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT > s_Hyman_01_2 > 10 8111431 . C <X> 0 . > DP=293;I16=226,65,0,0,8745,264919,0,0,17194,1.02329e+06,0,0,5567,124891,0,0;QS=1,0;MQSB=0.999726;MQ0F=0 > PL 0,255,255 > 10 8111432 . T C,<X> 0 . > DP=295;I16=228,65,1,0,9008,278800,13,169,17314,1.03049e+06,60,3600,5663,127373,11,121;QS=0.998554,0.00144637,0;SGB=-0.379885;RPB=1;MQB=1;MQSB=0.999532;BQB=1;MQ0F=0 > PL 0,255,255,255,255,255 > 10 8111433 . C <X> 0 . > DP=292;I16=220,68,0,0,8553,257087,0,0,17026,1.01379e+06,0,0,5605,126645,0,0;QS=1,0;MQSB=0.999234;MQ0F=0 > PL 0,255,255 > -bash-4.1$ > > > Totally missing. > > > Does anyone have a suggestion for discovering the deletion in the second > bamfile? > > > Best regards, > Jonathan > 3 Attachments >
------------------------------------------------------------------------------
_______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
