issue with mapped file

Question

[priya120195]

i really want to know why i am getting a deletion in vcf file but its not present in my bam file when i am visulaising it by igv

[Pierre Lindenbaum]

poorly asked question: how did you call the deletion ? what is it's size ? how did you checked it's not in igv ? How To Ask Good Questions On Technical And Scientific Forums

[priya120195]

i generated my bam files and vcf files by dragen tool to find the variants. Then i annotated my vcgf files.I got 12 bp deletion in the responsible gene in all my vcf files.So i just cross checked my bam files if that region is present in mapped files or not.It should be present in bam files but its not there. My question is ,how I am getting this variant if that region is not present in bam file ,i checked with samtools view too.

[Pierre Lindenbaum]

show us some SAM reads in this 12bp region please.

[priya120195]

THIS IS VCF FILE : zcat HL_intersection.vcf.gz |grep "90775878"

chr1    90775878    .   GGGACTGCTGGCTTAGCAGGGACTGGCTTAGCAGCAGCTGGCTGAGGAGGGGCTGGCTGAGCA G   31.95   PASS    .   GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB:PS 0|1:30,12:0.286:42:14,7:16,5:32:66,0,50:31.95,0.002796,53:0,34,37:12,18,5,7:14,16,4,8:90775876

BAM FILE :

GGAGGGGCTGGCTGAGCGGGGACTGCTGGCTTAGCAGGGACTGGCTTAGCAGCAGCTGGCTGAGGAGGGGCTGGCTTAGCGGGGGCTGGTCTTACAGAAGCTG :FF:FF,FFFFFFF:FFFF:FFFFF:FFF:FFFFFFF:FF,FFF:FFFFFFFFF:FFFFFFF:FF:FFFFFFFFFFFFFFFFF:FFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF RG:Z:RG0    AS:i:141    XS:i:114    NM:i:2  XQ:i:75
A00573:45:H7LK2DRXX:2:2253:17309:32597  147 chr1    90775877    60  151M    =   90775644    -384    AGGGACTGCTGGCTTAGCAGGGACTGGCTTAGCAGCAGCTGGCTGAGGAGGGGCTGGCTGAGCGGGGACTGCTGGCTTAGCAGGGACTGGCTTAGCAGCAGCTGGCTGAGGAGGGGCTGGCTTAGCGGGGGCTGGTCTTACAGAAGCTGTC FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF RG:Z:RG0    AS:i:146    XS:i:117    NM:i:1  XQ:i:84
A00573:45:H7LK2DRXX:2:1273:4065:17738   99  chr1    90775882    60  151M    =   90776027    296 CTGCTGGCTTAGCAGGGACTGGCTTAGCAGCAGCTGGCTGAGGAGGGG
CTGGCTGAGCGGGGACTGCTGGCTTAGCAGGGACTGGCTTAGCAGCAGCTGGCTGAGGAGGGGCTGGCTTAGCGGGGGCTGGTCTTACAGAAGCTGTCTGGGC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF RG:Z:RG0    AS:i:146    XS:i:112    NM:i:1  XQ:i:95
A00573:45:H7LK2DRXX:1:1141:7780:24862   147 chr1    90775883    60  151M    =   90775677    -357    TGCTGGCTTAGCAGGGACTGGCTTAGCAGCAGCTGGCTGAGGAGGGGCTGGCTGAGCAGGGACTGCTGGCTTAGCAGGGACTGGCTTAGCAGCAGCTGGCTGAGGAGGGGCTGGCTTAGCGGGGGCTGGTCTTACAGAAGCTGTCTGGGCA FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF RG:Z:RG0    AS:i:151    XS:i:116    NM:i:0  XQ:i:104
A00573:45:H7LK2DRXX:1:2222:18855:16454  163 chr1    90775896    60  151M    =   90776197    452 GGGACTGGCTTAGCAGCAGCTGGCTGAGGAGGGGCTGGCTGAGCAGGG
ACTGCTGGCTTAGCAGGGACTGGCTTAGCAGCAGCTGGCTGAGGAGGGGCTGGCTTAGCGGGGGCTGGTCTTACAGAAGCTGTCTGGGCAGGGGCTGGCTGAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF

[Pierre Lindenbaum]

what was the command used to extract the reads from the BAM file ?