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
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