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Posts by 1097049297
... I want to annotate VCF with HGMD database information by **sql**, but there is some problem with indel records, such as : >In VCF the variant is `5 13868103 . TA T`, >but in HGMD, it becomes `5 13868104 A .` So for annotation correct, should I change variants like `5 13868103 . TA T` to `5 1 ...
Comment: A: extracting reads from bam file
... As pciifen said, region format is chr:start-stop, like "chr3:1000-2000" ...
... I want to extract reads with a known variant form a bam file, I have tried like below: ```bash $samtools -q 30 view | grep -i # reference pattern is AA[C]TCG ``` However maybe it would be some problem like if a SNP in the pattern or recurrent pattern in reads So if any one know some better wa ...
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