Entering edit mode
4.3 years ago
sami
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40
Using FreeBayes i get vcf file without DP4 field!
How can i force DP4 to be present in my vcf.
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Who says you need that field?
Your question needs a lot of context. Please give us that context so we can help you better.
DP4 gives depth of coverage in reverse and foward strain. if there is mutation in fowards but not in reverse , we can't take it. normally , if mutation exist in foward , it must be present also in reverse. We use Depth because we can't filter variant using mapp quality . MAPQ is not a good filter. height value of MAPQ can eliminate some variants implicitly! if you think i can use MAPQ, so how ? if you have annoter filter , so give it to me ! so i would like also to know the main difference between bcftools and FreeBayes. thank you
Most references to DP4 that I can find online are from 4-5 years ago. Are you sure this attribute is still maintained in current VCF spec?
yes, you can get it using the new version of bcftools ,
Not sure if this helps, but bcftools documentation says that
FORMAT/DP4has been deprecated in favor ofFORMAT/ADFandFORMAT/ADR.You may also want to take a look at this thread that discusses this issue - the thread has input from Heng Li (who developed samtoolls) as well as Erik Garrison (developer of Freebayes). You may get some leads from there.