Question: bcftools call error "--gvcf output mode requires FORMAT/DP tag, which is not present in the input header"
0
gravatar for AGE
10 months 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 • 530 views
ADD COMMENTlink modified 10 months ago • written 10 months ago by AGE20

your input does not appear to have any header

ADD REPLYlink written 10 months ago by steve2.6k
2
gravatar for Pierre Lindenbaum
10 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum129k 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 10 months ago by Pierre Lindenbaum129k
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