I have a multi-sample VCF file and the Kaviar VCF file. I'm doing:
bedtools intersect -sorted -a Family5_sorted.vcf.gz -b Kaviar-150812-ISB-hg19.vcf.gz -wb
It prints 9795 results for chromosome 1 and then dies with a Segementation fault (core dumped). The line that it dies on doesn't seem to be any different than previous lines. I've also tried reversing the a and b file and it dies on a different line (but close to where it dies the other way avb is 627982 and bva is 625369). How do I troubleshoot what's going on?