Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

Tribble can't find #CHROM header, but line is present



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    Jess McLaughlin

    Hello! I figured it out, and thought I should post a follow-up. Basically, there was a random white-space character in my variables that wasn't visible to me, so when the output gvcf was created with the default "here's the command you used" line, it prematurely split that line, signaling that the actual variant data was starting there (when obviously it wasn't). So if you, random person who has found this post in your google results, are dealing with a similar issue, check for that. Good luck!

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    Laura Gauthier

    Thanks for posting your solution Jess McLaughlin!  I have been known to open VCFs with vim and do a couple tricks to do what MS Word used to call "reveal codes":

    :set listchars=eol:$,tab:>-,trail:~,extends:>,precedes:<

    then :set list

    and this should turn all the spaces, tabs, and newlines into visible characters, which has also solved many 4 spaces != tab issues.

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