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.