Question: how to judge the genotype for the postion with 'rs8175347' ?
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gravatar for kaixian110
7 months ago by
kaixian1100
kaixian1100 wrote:

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

sequencing snp indel • 259 views
ADD COMMENTlink modified 7 months ago by Kevin Blighe21k • written 7 months ago by kaixian1100
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gravatar for Kevin Blighe
7 months ago by
Kevin Blighe21k
University College London Cancer Institute
Kevin Blighe21k wrote:

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

ADD COMMENTlink modified 7 months ago • written 7 months ago by Kevin Blighe21k
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