User: Max

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Max130
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Posts by Max

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Comment: C: Want to Skip Annotation Step (in MutSig_preprocess)
... 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 16 months ago by Max130
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generating categ in mutation table for MutSigCV
... 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 ...
mutsigcv written 16 months ago by Max130
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Comment: C: Is there a tool for counting the number of non-synonymous sites in a CDS
... Thanks. I posted the same question nearly a year ago and forgot both about it and the response. ...
written 16 months ago by Max130
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Is there a tool for counting the number of non-synonymous sites in a CDS
... 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 ...
cds biomart dnds ensembl written 16 months ago by Max130 • updated 16 months ago by natasha.sernova2.6k
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Comment: C: required data files and dependences to run maf2maf and maf2vcf
... 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 17 months ago by Max130
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required data files and dependences to run maf2maf and maf2vcf
... 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 ~ ...
maf2vcf vcf2maf maf2maf written 17 months ago by Max130
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baserecalibrator error: Unable to find color space information in SOLiD read
... 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 ...
gatk baserecalibrator written 17 months ago by Max130
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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 17 months ago by Max130
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bwa samse: invalid option 'R'
... 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, ...
bwa written 17 months ago by Max130 • updated 17 months ago by WouterDeCoster23k
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Comment: C: How do I find input arguments (RGPU, RGLB, etc) for AddOrReplaceReadGroups
... 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 18 months ago by Max130

Latest awards to Max

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Popular Question 2.1 years ago, created a question with more than 1,000 views. For Are There "Standard" Quality Score Cutoffs For Gatk Vcf'S
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Obtaining All Cds Sequences (I.E. All Spliced Exon Variants) From Ucsc
Popular Question 2.1 years ago, created a question with more than 1,000 views. For problems updating biomaRt in R version 3.0
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Are There "Standard" Quality Score Cutoffs For Gatk Vcf'S
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Exon Phase And Start Codon

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