Question: bcftools call error "--gvcf output mode requires FORMAT/DP tag, which is not present in the input header"
0
gravatar for AGE
16 days ago by
AGE20
AGE20 wrote:

I would like to get non-variant sites using bcftools but am getting an odd error about the DP field.

bcftools  mpileup -f genomic.fa file.bam | bcftools call --gvcf 5 -m > gvcf.vcf

--gvcf output mode requires FORMAT/DP tag, which is not present in the input header

Yet, the DP field is clearly in the output of mpileup:

NW_006532014.1  14714   .       A       <*>     0       .       DP=52;I16=26,17,0,0,1926,98680,0,0,2580,154800,0,0,750,16322,0,0;QS=1,0;MQSB=1;MQ0F=0   PL      0,129,255
NW_006532014.1  14715   .       T       <*>     0       .       DP=53;I16=27,18,0,0,1959,97077,0,0,2700,162000,0,0,794,17716,0,0;QS=1,0;MQSB=1;MQ0F=0   PL      0,135,255
NW_006532014.1  14716   .       A       <*>     0       .       DP=50;I16=25,19,0,0,1905,91787,0,0,2640,158400,0,0,790,17884,0,0;QS=1,0;MQSB=1;MQ0F=0   PL      0,132,255
NW_006532014.1  14717   .       T       <*>     0       .       DP=50;I16=25,18,0,0,1841,88215,0,0,2580,154800,0,0,766,17490,0,0;QS=1,0;MQSB=1;MQ0F=0   PL      0,129,255

Any idea what is the problem? When getting variant sites with -vm there is no issue. What I want is the DP4 field on a gvcf file, are the relevant numbers the first 4 after I16= ?

Thanks!

Answer:

 bcftools  mpileup -f genomic.fa file.bam -a "AD,ADF,ADR,DP,SP,INFO/AD,INFO/ADF,INFO/ADR" | bcftools call --gvcf 5 -m > gvcf.vc
snp sequence • 121 views
ADD COMMENTlink modified 15 days ago • written 16 days ago by AGE20

your input does not appear to have any header

ADD REPLYlink written 16 days ago by steve2.3k
2
gravatar for Pierre Lindenbaum
16 days ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum123k wrote:

https://samtools.github.io/bcftools/bcftools.html#mpileup

try to specify --gvcf 5 and --annotate in mpileup

annotate: Comma-separated list of FORMAT and INFO tags to output. (case-insensitive, the "FORMAT/" prefix is optional, and use "?" to list available annotations on the command line) [null]:

ADD COMMENTlink written 16 days ago by Pierre Lindenbaum123k
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: 2079 users visited in the last hour