bedtools expects "chr1" in VCF where reference data uses "1"

[aksarkar]

This means intersect, etc. all give nonsense answers.

A minimal test case:

#!/bin/bash
cat <<EOF >test1.vcf
##fileformat=VCFv4.0
1   10000   foo A   C   .   .   .
EOF
cat <<EOF >test2.vcf
##fileformat=VCFv4.0
chr1    10000   foo A   C   .   .   .
EOF
echo -e 'chr1\t0\t20000' >test.bed
bedtools intersect -a test1.vcf -b test.bed >test1.hits
bedtools intersect -a test2.vcf -b test.bed >test2.hits
head *.hits

And its output

==> test1.hits <==

==> test2.hits <==
chr1    10000   foo     A       C       .       .       .