Bedtools intersect vcf and bed files

Question

[User000]

Hello,

I am trying to intersect my vcf files with a bed file using bedtools. I divided my genome by chromosomes prior variant calling.

bedtools intersect -a input.vcf -b input.bed -header -wa output.vcf
bcftools annotate -a input.bed -c CHROM,FROM,TO,GENE -h <(echo '##INFO=<ID=GENE,Number=1,Type=String,Description="Gene name">') output.vcf > output.outvcf

I get the following error:

[E::sam_parse1] missing SAM header
[W::sam_read1] Parse error at line 1

What should I worry about?

PS. Nonetheless the error I get and output vcf files, but I want to be sure everything is running OK, and why I get those error.

[Arup Ghosh]

Do your intersection script also contains variant calling commands?

[User000]

Actually in the header I see variant calling commands.. I guess this is OK, intersection script has only those two commands

[Arup Ghosh]

Looks like the variant calling tool(mpileup) is throwing the error, just comment out the unnecessary lines.

[User000]

it is actually commented out in the header no?

##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##bcftoolsVersion=1.10.2-18-g5774f32+htslib-1.10.2-22-gbfc9f0d
##bcftoolsCommand=mpileup -r chr3:1-5000 --threads 6 -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -f genome.fasta --bam-list bam_list --excl-flags UNMAP,SECONDARY,QCFAIL,DUP --min-MQ 20
##reference=file://genome.fasta

[Arup Ghosh]

I mean comment out the variant calling commands in your script.

[User000]

but my script has only the above mentioned commands...intersect and annotate.. sorry I am a bit confused :/