User: dec986
dec986 • 210
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Posts by dec986
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Comment:
C: Building Dict File for GATK
... this was a comedy of errors on my part, I seemed to have clicked every wrong button and done everything wrong on the way. Thanks for your help ATpoint! ...
written 5 days ago by
dec986 • 210
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... I'm going through the instructions page on https://gatkforums.broadinstitute.org/gatk/discussion/1601/how-can-i-prepare-a-fasta-file-to-use-as-reference
Specifically, the command I don't see how to do is:
java -jar CreateSequenceDictionary.jar R= Homo_sapiens_assembly18.fasta O= Homo_sapiens_ ...
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... the files are of different lengths. I just ended up using a Perl hash, which was much easier. ...
written 9 days ago by
dec986 • 210
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... they don't have identical sort order :( ...
written 10 days ago by
dec986 • 210
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... I have a list of VCFs that I'm converting from gVCF to VCF thus:
zcat HG00096.final_combined.g.vcf.gz | gvcftools-0.17.0/bin/break_blocks --region-file gsa_positions.chromEnd_plus1.bed --ref g1k_v37/human_g1k_v37.fasta --exclude-off-target > vcf/HG00096.bb.vcf 2> break_blocks_err/HG00096. ...
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... I'm attempting to create a region file for break_blocks, which has a very specific format requirement
for example:
1 1272857 1272858 ZYX-rs77443780 . C T
1 1273477 1273478 seq-rs797044834 . GGGGGCAGCCGGGT G
but this issue is that I don't think that the last end `1273478` is correct. Thi ...
written 4 weeks ago by
dec986 • 210
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... the problem is that at some point vcftools stops making the output file, and switches the important info to STDERR. I've never seen another program do this before. ...
written 4 weeks ago by
dec986 • 210
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... I'm running a test now, it should finish in about a day I think (on a small data set) ...
written 4 weeks ago by
dec986 • 210
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... I thought that it might be my perlbrew installation, but that doesn't appear to be the case. The first cycle of parallel runs writes the log files, after that, no more log files, and no explanation. The commands are run *identically*. Looks like I have to give those other programs a try. Thanks ...
written 4 weeks ago by
dec986 • 210
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... unfortunately, that didn't change anything. Is vcftools really the only tool available that can calculate Fst? This problem sounds so trivial, but it's useless without that log file. ...
written 4 weeks ago by
dec986 • 210
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