samtools
Bcftools annotate overwrite existing tag
Hi,
I am trying to add the FORMAT/DP tag to a vcf taking the depth information from a bed file. I only want to add the tag if not already present in the vcf.
The code I am using is the following:
echo -e '##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">' >> hdr.txt
bcftools annotate -a coverage.bed.gz -h hdr.tx -c CHROM,FROM,TO,+FORMAT/DP sample.vcf.gz | bgzip > sample.DP.vcf.gz
The coverage.bed.gz looks like the following:
zcat coverage.bed.gz
chr1 10000 10005 0
chr1 10005 10008 3
chr1 10008 10019 4
chr1 10019 10035 6
chr1 10035 10052 7
chr1 10052 10094 8
chr1 10094 10106 7
chr1 10106 10109 5
chr1 10109 10110 4
chr1 10110 10118 1
I tested both 1.15.1 and 1.10.2 versions.
Even if using the "+TAG" option, the FORMAT:DP is overwritten even if it already exists. Here an example:
Original file:
chr1 10904 . G A 15.93 PASS AC=2;AF=1.000;AN=2;DP=11;FS=0.000;MQ=28.72;MQRankSum=1.733;QD=4.23;ReadPosRankSum=0.480;SOR=0.859;FractionInformativeReads=0.909 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB:PS 1|1:2,8:0.8000:10:1,5:1,3:8:53,12,0:1.5931e+01,9.3190e+00,6.6765e-01:0.00,34.77,37.77:0,2,5,3:1,1,8,0:10904
Output file:
chr1 10904 . G A 15.93 PASS AC=2;AF=1;AN=2;DP=11;FS=0;MQ=28.72;MQRankSum=1.733;QD=4.23;ReadPosRankSum=0.48;SOR=0.859;FractionInformativeReads=0.909 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB:PS 1|1:2,8:0.8:0:1,5:1,3:8:53,12,0:15.931,9.319,0.66765:0,34.77,37.77:0,2,5,3:1,1,8,0:10904
As you can see, the value 10 is replaced with 0.
Is this an expected behaviour? How can i avoid that and obtain the wanted result?
Thanks, Valentina
What is the version of bcftools you are using? I just tested with the latest and it seems to be working as expected.
Hi @pd3
I tested both 1.15.1 and 1.10.2 bedtools versions, since I had these already installed. I'll test as soon as I can the latest version and let you know!
i am also finding similar behavior for bcftools annotate with bcftools v1.9, when applying to format fields. is there any update here?
We are at version of bcftools 1.21, please update http://samtools.github.io/bcftools/howtos/install.html