User: Max
Max • 140
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Posts by Max
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... I'm having the same problem running MutSigCV (i.e. line 184 error when calling MutSigCV(mutationfile,coverage,covariates,output,dictionary,chr19ref) ). Would you mind providing me with some more detail about the hack that proved to be a successful work-around for you? From your description, it seems ...
written 4.2 years ago by
Max • 140
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... I have two questions about how to compute the MutSigCV mutation table's categ values:
1. The documentation mentions that if this field is not specified in the existing maf, it can be computed using the pre-processing function of MutSigCV. However, no information is provided on how to execute this p ...
written 4.2 years ago by
Max • 140
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... Thanks. I posted the same question nearly a year ago and forgot both about it and the response. ...
written 4.2 years ago by
Max • 140
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... In order to compute dn/ds (the ratio of synonymous to non-synonymous substitutions in a mutated sequence), I need to first calculate the number of synonymous and non-synonymous sites in a coding sequence. I've been doing this rather tediously the "brute force" way, i.e. obtaining exons for each codi ...
written 4.2 years ago by
Max • 140
• updated
4.2 years ago by
natasha.sernova • 3.7k
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... The input is a maf file (derived from mutect vcf using someone else's script).
In any case, the problems that I'm experiencing seem to be due to a failure to obtain/install the reference data for VEP. ...
written 4.2 years ago by
Max • 140
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... I have been attempting to use maf2maf to filter maf's generated from mutect output vcf's. I was under the impression that other than the input maf file, the only necessary reference file is the human genome fasta, i.e.
perl maf2maf.pl --input-maf oldmaf.maf --output-mas newmaf.maf --ref-fasta ~ ...
written 4.2 years ago by
Max • 140
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... When running GATK baserecalibrator on SOLiD read data, I initially obtained the following error:
ERROR MESSAGE: SAM/BAM/CRAM file htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter@7cc9970a is malformed. Please see http://gatkforums.broadinstitute.org/discussion/1317/collected-fa ...
written 4.3 years ago by
Max • 140
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Comment:
C: bwa samse: invalid option 'R'
... Right, I think I was confusing the -R for read groups in bwa mem (-r is something else) with -r for reads in bwa sampe ...
written 4.3 years ago by
Max • 140
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... When creating .bam files from single-end read fastq's, I ran into difficulties with mutect because the .bam files didn't contain read groups. I attempted to recreate the .bams by rerunning bwa samse with the -R option, but I get an error stating that -R is an invalid option with samse (in contrast, ...
written 4.3 years ago by
Max • 140
• updated
4.3 years ago by
WouterDeCoster ♦ 44k
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... I had looked at that, but the barcodes for each read aren't unique. I assumed that somewhere there is a unique barcode for the sample as well. In any case, I attempted to run addorreplaacereadgroups with RGPU=NONE, it gave an output .bam file, but it seems to be missing some identifiers in the heade ...
written 4.3 years ago by
Max • 140
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