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How to change @SQ file in a .bam file
I am trying to run GATK to get a g.vcf file using an interval list.
I get the following message:
ERROR MESSAGE: File associated with name interval.list is malformed: Interval file could not be parsed in any supported format. caused by Failed to parse Genome Location string: gi|409893163|gb|CP003904.1| : 74250-75830
In my .bam file I have the following:
@SQ SN:gi|409893163|gb|CP003904.1| LN:1667892
How can I change this to read:
@SQ SN:CP003904.1 LN:1667892
My genome is a bacteria
I don't think GATK like the "|" in my files. Or is there some way to change my interval.list