Bedtools intersection

Question

[rejoeraymond776]

While intersecting a VCF file and bed to obtain the reads that map to a class of genes, bedtools gives the following error:

***** WARNING: File TARGT_First.bed has inconsistent naming convention for record: chr1 45794952    45795134    MUTYH   1

***** WARNING: File TARGT_First.bed has inconsistent naming convention for record: chr1 45794952    45795134    MUTYH   1

The command is:

bedtools intersect -a class.bed -b meron.vcf -wb

How to resolve this?

Thank you!

Answer 1

[Pierre Lindenbaum]

it's just a warning. This message is usually displayed when you have a mix of chromosomes with or without the prefix 'chr'. Issue with naming convention in bedtools ; How to Bedtools intersect two different sorted BED files ; etc...