Brad Chapman chapmanb
chapmanb
/ gatk_vcfsimplify-orig.vcf
Created
December 14, 2011 11:29
GATK VCF over-simplification of multiple alleles example
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| ##fileformat=VCFv4.1 | |
| #CHROM POS ID REF ALT QUAL FILTER INFO | |
| 6 58777178 . GG G,TG 106.357 . . |
chapmanb
/ biostar_challenge_ZC3H7B.vcf
Created
December 21, 2011 20:46
BioStar Challenge variants in ZC3H7B
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| child_111217_biostar-variants.vcf:chr22 41742029 . T A 201.60 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=3.515;DP=22;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=6.7867;MQ=48.95;MQ0=0;MQRankSum=0.853;QD=9.16;ReadPosRankSum=0.853;SNPEFF_AMINO_ACID_CHANGE=C/*;SNPEFF_CODON_CHANGE=tgT/tgA;SNPEFF_EFFECT=STOP_GAINED;SNPEFF_EXON_ID=exon_22_41742007_41742212;SNPEFF_FUNCTIONAL_CLASS=NONSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=ZC3H7B;SNPEFF_IMPACT=HIGH;SNPEFF_TRANSCRIPT_ID=ENST00000351589;set=child_111217_biostar-sort-dup-gatkrecal-realign-variants-snp-filterSNP GT:AD:DP:GQ:PL 0/1:8,14:22:1.52:230,0,2 | |
| child_111217_biostar-variants.vcf:chr22 41742047 . C G 71.96 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=-0.972;DP=19;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=6.7516;MQ=48.19;MQ0=0;MQRankSum=-2.071;QD=3.79;ReadPosRankSum=0.972;SNPEFF_AMINO_ACID_CHANGE=C/W;SNPEFF_CODON_CHANGE=tgC/tgG;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_22_41742007_41742212;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_codin |
chapmanb
/ updated_GlobPipe.py
Created
December 28, 2011 10:53
Update GlobPipe for recent Biopython versions: http://biostar.stackexchange.com/questions/15800/fasta-module-in-python-biopython
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| def runGlobPlot(): | |
| try: | |
| smoothFrame = int(sys.argv[1]) | |
| DOM_joinFrame = int(sys.argv[2]) | |
| DOM_peakFrame = int(sys.argv[3]) | |
| DIS_joinFrame = int(sys.argv[4]) | |
| DIS_peakFrame = int(sys.argv[5]) | |
| file = str(sys.argv[6]) | |
| db = open(file,'r') | |
| except: |
chapmanb
/ DisEMBL-SeqIO.py
Created
January 25, 2012 11:50
Update DisEMBL (http://dis.embl.de/) for recent Biopython versions: http://biostar.stackexchange.com/questions/16673/fasta-module-in-biopython-python-again
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| #!/usr/local/bin/python | |
| # Copyright (C) 2004 Rune Linding & Lars Juhl Jensen - EMBL | |
| # The DisEMBL is licensed under the GPL license | |
| # (http://www.opensource.org/licenses/gpl-license.php) | |
| # DisEMBL pipeline | |
| from string import * | |
| from sys import argv | |
| from Bio import SeqIO | |
| import fpformat |
chapmanb
/ SelectVariants-discordance.patch
Created
January 28, 2012 17:15
GATK SelectVariants --discordance: check comparison genotypes
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java | |
| index 6d94ffe..1d6a7f7 100755 | |
| --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java | |
| +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java | |
| @@ -557,7 +557,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR | |
| // Look for this sample in the all vcs of the comp ROD track. | |
| boolean foundVariant = false; | |
| for (VariantContext compVC : compVCs) { | |
| - if (sampleHasVariant(compVC.getGenotype(g.getSampleName()))) { | |
| + if (haveSameGenotypes(g, compVC.getGenotype(g.getSampleName()))) { |
chapmanb
/ AbstractVCFCodec_Allele-breakends.patch
Created
February 21, 2012 02:16
GATK support for breakend alleles
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java | |
| index e44c10f..3c498c8 100755 | |
| --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java | |
| +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java | |
| @@ -540,12 +540,15 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec { | |
| } | |
| /** | |
| - * return true if this is a symbolic allele (e.g. <SOMETAG>) otherwise false | |
| + * return true if this is a symbolic allele (e.g. <SOMETAG>) or |
chapmanb
/ spp_peak_call.R
Created
March 21, 2012 18:49
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # Perform peak calling with Peter Park's SPP | |
| # http://compbio.med.harvard.edu/Supplements/ChIP-seq/tutorial.html | |
| library(spp) | |
| align.dir <- "/store3/projects/Oettinger/mouse/solexa/ToshiAnalysis/alignments" | |
| cur.analysis <- "lane1" | |
| chip.file <- file.path(align.dir, "lane1_sample4_pml3_10.uniq.ilt.qltout.onehead") | |
| back.file <- file.path(align.dir, "lane8_TIC_pml3_10.uniq.ilt.qltout.onehead") |
chapmanb
/ process_calls-allow_ns.patch
Created
August 22, 2012 18:36
cortex_var patch to allow reference base Ns in discovered indels
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| --- scripts/analyse_variants/process_calls.pl.orig 2012-08-17 11:49:14.000000000 -0400 | |
| +++ scripts/analyse_variants/process_calls.pl 2012-08-22 13:02:23.612425014 -0400 | |
| @@ -1754,17 +1754,17 @@ | |
| my $two_alleles = $aref_indel_alleles->[ $cnt - 1 ]; | |
| my $this_indel_ref_allele; | |
| my $this_indel_alt_allele; | |
| - if ( $two_alleles =~ /^([ACGT]+)_([ACGT]+)$/ ) | |
| + if ( $two_alleles =~ /^([ACGTN]+)_([ACGTN]+)$/ ) | |
| { | |
| $this_indel_ref_allele = $1; |
chapmanb
/ dpsample_nullallele.patch
Created
August 27, 2012 10:50
Fix GATK null allele error when calculating DepthPerAlleleBySample for indels
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java | |
| index 5d83ddd..928d836 100755 | |
| --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java | |
| +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java | |
| @@ -87,12 +87,12 @@ public class DepthPerAlleleBySample extends GenotypeAnnotation implements Standa | |
| for ( PileupElement p : pileup ) { | |
| if ( p.isBeforeInsertion() ) { | |
| - | |
| - final Allele insertion = Allele.create((char)refBase + p.getEventBases(), false); |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| #!/usr/bin/env python | |
| ''' | |
| FastQC checker for Galaxy biomedical data analysis platform | |
| @author: Ilya Sytchev | |
| Input: one or more files in fastq format | |
| Output: sequencing quality report in text format |