"Could not parse the header line:... " Problem: The problem can be due to a comma in the gene/contig ID gi|3656203|ref|NZ_CM002351|:c1052230-105140,c1051398-1051048 Samtools mpileup is adding information to the original contig ID separated by comma. ...CONTIG,length=1543,IDX=923609> and gets confused if the gene ID already includes a comma: 1005929-1007642,1007542-1008571 Solution: Remove all comma from your gene or contig ID names before running samtools. |