Bcftools how to add DP to FORMAT field (get per sample read depth for REF vs ALT alleles )
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9 weeks ago
Linda ▴ 30

I'm trying to achieve what this post was looking for Add Dp Tag To Genotype Field Of Vcf File

Currently this is my command:

bcftools mpileup -Ou --max-depth 8000 --min-MQ 30 --min-BQ 30 -f reference.fasta sample1.sorted.bam | bcftools call --ploidy 1 -Ou -mv |  bcftools filter -s LowQual -e \'%QUAL<20\'  > sample1.flt.vcf

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  sample1.sorted.bam
Imtechella_halotolerans_length_3113269  4051    .   C   T   41.4148 PASS    DP=2;VDB=0.02;SGB=-0.453602;MQ0F=0;AC=1;AN=1;DP4=0,0,0,2;MQ=42  GT:PL   1:71,0
Imtechella_halotolerans_length_3113269  4081    .   C   T   45.4146 PASS    DP=2;VDB=0.02;SGB=-0.453602;MQ0F=0;AC=1;AN=1;DP4=0,0,0,2;MQ=42  GT:PL   1:75,0

As far as I can understand the DP specified in the INFO is depth of coverage across all samples. How can I get the depth per sample info in the format/genotype field?

Any help appreciated!

bcftools snp vcf calling • 569 views
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9 weeks ago

Hi, you can specify this via the mpileup command. Please take a look at this snippet from my historical pipeline:

That is:

bcftools mpileup \
--redo-BAQ \
--min-BQ 30 \
--per-sample-mF \
-f "${Ref_FASTA}" \ Aligned_Sorted_PCRDuped_FiltMAPQ.bam |\ bcftools call \ --multiallelic-caller \ --variants-only \ -Ob > Aligned_Sorted_PCRDuped_FiltMAPQ.bcf ; Kevin ADD COMMENT 1 Entering edit mode Brilliant thanks Kevin ADD REPLY 0 Entering edit mode Hi Kevin, sorry to dredge up an old question. I used your annotate code snippet above and now my FORMAT col is: GT:PL:DP:SP:ADF:ADR:AD Is it possible to add GQ - genotype quality to this field? I tried adding FORMAT/GQ to the code above --annotate FORMAT/GQ,FORMAT/AD,FORMAT/ADF,FORMAT/ADR,FORMAT/DP,FORMAT/SP,INFO/AD,INFO/ADF,INFO/ADR but it's saying could not parse tag "FORMAT/GQ" Thanks so much! :) ADD REPLY 0 Entering edit mode Hi Linda, I was not sure; so, had to search. It seems that GQ is added during the subsequent bcftools call command: -f, --format-fields <list> output format fields: GQ,GP (lowercase allowed) [] Found via this answer: How to get GQ after running BCFTools? ADD REPLY 1 Entering edit mode Hey thanks for your help, I found that link too. All good! ADD REPLY 0 Entering edit mode Hey, I used your annotate code Is it possible to add AO and RO? I used this command: bcftools mpileup \ --annotate FORMAT/AD,FORMAT/ADF,FORMAT/ADR,FORMAT/DP,FORMAT/AO,FORMAT/RO,FORMAT/SP,INFO/AD,INFO/ADF,INFO/ADR \ -O b -o$OUTPUT_BCF_F1 \

and I got: Could not parse tag "FORMAT/AO"

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I don't believe AO and RO are in any way standard / common tags. Where have you seen them previously? - freebayes? As far as I am aware, they relate to a somatic variant context; so, there is no way for bcftools to calculate them from just a VCF (need the original BAMs).

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I am trying to run VcfSampleCompare, and I get warnings as you can see in this link: https://github.com/hepcat72/vcfSampleCompare/issues/26

Robert is sayings that my vcf file is missing DP,AO,RO tags and I need to add the DP tag. After adding the DP tag, usings your script , I had another warning so I think maybe I need the AO RO too..