Hello, In these days ,I got a question about how to judge the genotype for the specified position with using a sample BAM file . perhaps it's easy to judge SNV ,but maybe to judge INDEL is hard to complete. For example , for the rs8175347 , which one in these genotypes '6TA/7TA' or '7TA/7TA' or '6TA/6TA' should be judged as the genotype of the sample (input bam file format) ??
best wishes
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written
by
kaixian110 •
1 answer
If you have a VCF that lists variants called over the BAM, then the actual variant allele(s), i.e., variant genotypes, should appear in the ALT column in the VCF
If you want to look at the sequences directly in the BAM, output over the exact reference genome co-ordinates of interest with:
samtools view MyBam.bam 2:234668881-234668883
or
samtools view MyBam.bam chr2:234668881-234668883
'2:234668881-234668883' is 1bp flanking around your SNP of interest. If there are insertions present, then they should still be output as the co-ordinate relate to the reference genome.
Co-ordinates that I've used here are hg19 / GRCh37
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