Bedtools intersection
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!
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Pierre Lindenbaum
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rejoeraymond776 •
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written
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rejoeraymond776 •
1 answer
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...
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Pierre Lindenbaum
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