Could not parse a VCF file when using bcftools annotate

Question

[ManuelDB]

I am not sure If I am doing something wrong ( I don't think so based on the documentation)

I have a VCF file and I want to remove the SB flag and annotated the variants with the 4th column of my bed file. The command is this

 apptainer exec --bind /mnt:/mnt docker://mgibio/bcftools-cwl:1.12 bcftools annotate \
          -a "$ampliconscoordenatesbed" \
          -c CHROM,FROM,TO,4 \
          -h "$RunID"_"$Sample_Name".vcf \
          -x FORMAT/SB "$RunID"_"$Sample_Name".vcf > "$RunID"_"$Sample_Name"_FINAL.vcf           

With this command I get this error

 Could not parse 240430_M01875_1088_000000000-LH8PT_W2407562-002.vcf: #CHROM     POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  240430_M01875_1088_000000000-LH8PT_W2407562-002.bam

The VCF file come directly from Pisces and I don't see any error.

My bed file looks good too

 chr1   43349260    43349367    MPL_003_F_
 chr1   43349260    43349367    MPL_003_R_
 chr1   45331526    45331640    MUTYH_002_F_
 chr1   45331526    45331640    MUTYH_002_R_

What am I doing wrong??

[Jeremy Leipzig]

what happens when you change the sample name from 240430_M01875_1088_000000000-LH8PT_W2407562-002.bam to sample1?

Answer 1

[ManuelDB]

Thank you for your question. It was me and the bad documentation of the programs. I make it run with this lines

apptainer exec --bind /mnt:/mnt docker://mgibio/bcftools-cwl:1.12 bcftools annotate \
         -x FORMAT/SB "$RunID"_"$Sample_Name".vcf > "$RunID"_"$Sample_Name"_withoutSB.vcf
rm "$RunID"_"$Sample_Name".vcf

apptainer exec --bind /mnt:/mnt docker://mgibio/bcftools-cwl:1.12 bcftools annotate \
        -a "$ampliconscoordenatesbed" \
        -c CHROM,FROM,TO,AMPLICON \
        -h <(echo '##INFO=<ID=AMPLICON,Number=1,Type=String,Description="Amplicon name">') \
        "$RunID"_"$Sample_Name"_withoutSB.vcf > "$RunID"_"$Sample_Name"_withoutSB_AmpliconNameAdded.vcf

I found part of the solution here Addin gene information to VCF file

[Ram]

bad documentation of the programs

Nope, the documentation is quite clear. -c clearly states that you need header lines if you are using a non VCF annotation file. You need not split the removal and addition into two commands, all you need to do is add the header line in your original code.