Entering edit mode
4.1 years ago
User000
▴
690
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.
Do your intersection script also contains variant calling commands?
Actually in the header I see variant calling commands.. I guess this is OK, intersection script has only those two commands
Looks like the variant calling tool(mpileup) is throwing the error, just comment out the unnecessary lines.
it is actually commented out in the header no?
I mean comment out the variant calling commands in your script.
but my script has only the above mentioned commands...intersect and annotate.. sorry I am a bit confused :/