I am trying to use the bedtools window command to obtain counts of the number of variants in each window of the hg19 human vcf files. Here is the command:
bedtools window -a 50kb.bed -b chr1.vcf.gz -c > coverage.txt
This results in the following error:
However, the command works fine on some of the smaller chromosomes (e.g. chr19) without the error occuring. What is causing this error and how can I stop it from happening?