Duplicate contig lines in merged header

tgen / vcfMerger2

Dynamic vcfMerger for 2 to N somatic variants vcf files

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Duplicate contig lines in merged header #2

Closed PedalheadPHX closed 5 years ago

PedalheadPHX commented 5 years ago

We need to fix the multiple headers, maybe add to the prep to correct the one to match the others

fileformat=VCFv4.2

fileDate=20190502

contig=

ChristopheLegendre commented 5 years ago

As I remember only one caller adds the string "assembly=GRCh38". Using a sed command should help us deal with this by removing the string at the Prep level

ChristopheLegendre commented 5 years ago

added a generic sed command to remove any additional information after assembly in the contig header lines.
added to the prep for vcf step.
added to the merging step as well