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J35P312 / TIDDIT

TIDDIT - structural variant calling
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Add TIDDIT cmd to version line in vcf header #2

Closed henrikstranneheim closed 6 years ago

J35P312 commented 7 years ago

Hello! I have now fixed a line for the TIDDIT command in the vcf header: TIDDITcmd="TIDDIT --sv -b few_reads" would you be happy with that? I made a new release 1.1.4, this time, I also updated the version tag in the TIDDIT sosurce code!

henrikstranneheim commented 7 years ago

Most important is that you write the version in the header

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18 maj 2017 kl. 16:53 skrev Jesper Eisfeldt notifications@github.com:

Hello! I have now fixed a line for the TIDDIT command in the vcf header: TIDDITcmd="TIDDIT --sv -b few_reads" would you be happy with that? I made a new release 1.1.4, this time, I also updated the version tag in the TIDDIT sosurce code!

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henrikstranneheim commented 7 years ago

You forgot to add the line according to vcf specifications, this throws errors:

TIDDITcmd="TIDDIT --sv -p 6 -o slask/ADM1059A2_lanes_8_sorted_md_brecal_tiddit -b slask/ADM1059A2_lanes_8_sorted_md_brecal.bam"

J35P312 commented 7 years ago

woopsie daisy! Which version are you using? I did forget the ## in version 1.1.4, but I fixed it for 1.1.5:

TIDDITcmd="TIDDIT --sv -b /proj/sens2016003/SWEGEN/bam//AB35001299.clean.dedup.bam -o /scratch/25774/TIDDIT/AB35001299.clean.dedup.tiddit"

Or do you get any other error?