Question: FreeBayes :the tag "DP4" is not defined in the VCF header
0
gravatar for sami
6 weeks ago by
sami20
sami20 wrote:

Using FreeBayes i get vcf file without DP4 field!

How can i force DP4 to be present in my vcf.

freebayes • 176 views
ADD COMMENTlink written 6 weeks ago by sami20

Who says you need that field?

ADD REPLYlink written 6 weeks ago by RamRS30k

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by sami20
1

i ask question , please if you don't have answer , don't write !

Your question needs a lot of context. Please give us that context so we can help you better.

ADD REPLYlink written 5 weeks ago by RamRS30k

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

ADD REPLYlink written 5 weeks ago by sami20
1

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?

ADD REPLYlink written 5 weeks ago by RamRS30k

yes, you can get it using the new version of bcftools ,

ADD REPLYlink written 5 weeks ago by sami20
3

Not sure if this helps, but bcftools documentation says that FORMAT/DP4 has been deprecated in favor of FORMAT/ADF and FORMAT/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.

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by RamRS30k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 592 users visited in the last hour