User: feltzmc

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feltzmc0
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Posts by feltzmc

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Comment: C: Empty SomaticSniper Output Files
... Interesting, I sorted the BAM and then used reheader, which would explain why the header says "none".  Samtools and the other tools I have used still accept this file as sorted (they don't tell me it needs to be sorted), so they must check some other aspect of the BAM to determine if it is sorted or ...
written 3.3 years ago by feltzmc0
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Comment: C: Empty SomaticSniper Output Files
... What makes you think its not sorted? ...
written 3.3 years ago by feltzmc0
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Comment: C: Empty SomaticSniper Output Files
... It does, we had to modify the the GRCh38 reference to add the capital CHR.  Figured that was easier than modifying all of the SAM files we had already created. ...
written 3.3 years ago by feltzmc0
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Empty SomaticSniper Output Files
... Hi all, I have a pipeline which I have written in python to do SNP calling and annotation.  The pipeline links Samtools, SomaticSniper, and SnpSift/SnpEff together to produce annotated VCF files for human cancer studies.  The inputs are two sorted indexed BAM files, and a human reference fasta file ...
somaticsniper snp written 3.3 years ago by feltzmc0 • updated 3.3 years ago by Jordan1.0k

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