Hi, I am trying to use bedtools intersect to intersect between a vcf and a bed file. My command is this
bedtools intersect -header -u -a ABC.vcf -b XYZ.bed > check.vcf
My bed file looks like this
chr6 29000001 33000000
But everytime I try this. It gives me the following error:
Error: Invalid record in file ABC.vcf. Record is chr6 60002 . A <*> 0 . DP=5;I16=5,0,0,0,191,7301,0,0,208,8656,0,0,47,495,0,0;QS=1,0;MQ0F=0 PL 0,15,104
I tried to remove this particular position and redo. But it gives error for the next position. What could be the issue here ? Any help would be appreciated.