How to set variant FILTER in a VCF file based on overlap with regions in a BED file

Question

[William]

How to set variant FILTER in a VCF file based on overlap with regions in a BED file?

I guess this should be possible using e.g. bcftools

But the bcftools filter command can't do this annotation direct.

http://samtools.github.io/bcftools/bcftools.html#filter

Seems like I first need to annotate the overlap in an INFO field.

http://samtools.github.io/bcftools/bcftools.html#annotate

Is there a way to set the FILTER status of a variant in 1 single command (without adding an INFO field) based on overlap of the variant with a region in a BED file?

Using bcftools or any other tool?

Answer 1

[Pierre Lindenbaum]

I wrote http://lindenb.github.io/jvarkit/VCFBedSetFilter.html

$java -jar dist/vcfbedsetfilter.jar --filter MYFILTER --blacklist in.bed in.vcf

Answer 2

[William]

I figured out how to do the annotation using BCFTools. 2 steps are needed.

Input BED file requires 1 for each region where the annotation should be set

Chr_01 1000 2000 1
Chr_05 5000 6000 1

Input header file:

##INFO=<ID=BAD_REGION,Number=0,Type=Flag,Description="My bad region for some reason">

bgzip and tabix the bed file

bgzip bad_regions.bed
tabix -p bed regions.bed.gz

First bcftools command to set the INFO field

bcftools annotate -a bad_regions.bed.gz  -h bad_regions.bed.hdr -c CHROM,FROM,TO,BAD_REGION  input.vcf.gz  -Oz -o output_w_INFO.vcf.gz

Second bcftools command to set the FILTER based on the INFO field

bcftools filter output_w_INFO.vcf.gz  -s BAD_REGION -m+ -e 'INFO/BAD_REGION=1' -Oz -o output_w_INFO_w_FILTER.vcf.gz

[Tiffany]

I tested and I think the last filtering should be:

bcftools filter output_w_INFO.vcf.gz  -s BAD_REGION -m+ -e 'INFO/BAD_REGION=1' | bcftools view -f PASS  -Oz -o output_w_INFO_w_FILTER.vcf.gz

In order to remove the BAD_REGION annotated SNPs.

[William]

I wanted to keep the BAD_REGION SNPs, but just tabel these SNPs.

If you just want to remove these SNPs, than it's much more straightforward to do something like bedtools subtract -a input.vcf -b bad_region.bed