python utilities to work with Variant Call Format files (VCF)
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Latest commit 36d89a0 Apr 1, 2014
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PythonNotebooks added chromInfo.bed Dec 5, 2012
docs updated usage vcf.gz instead of vcf Jun 12, 2013
Per_sample_variantEvalGenotypeConcordance.py Added code to check if the sample stubs of the gold and variant2 call… Aug 21, 2013
README.md added Twitter account :) Mar 26, 2014
VcfFile.py updated parseMetaLines function to parse lines that begin with ## but… Jan 16, 2014
VcfGenotype.py Added functions setFormatAndGstring and setFormatString Sep 6, 2013
VcfMetaLines.py added class MiscLines to represent lines that begin with ## but are n… Jan 16, 2014
VcfPed.py added back class and scripts python files Nov 20, 2012
VcfRecord.py added function overwriteFilter Oct 22, 2013
VcfSampleEval.py added methods write_genotype_matrix, incrementcellcount, boolean para… Mar 31, 2014
add-nonVariantVcfRecords.py removed debug print statement when reading bed file Mar 26, 2013
describe_vcf_filter_header.py added back class and scripts python files Nov 20, 2012
describe_vcf_format_header.py added back class and scripts python files Nov 20, 2012
describe_vcf_info_header.py added back class and scripts python files Nov 20, 2012
phred_scale.py added back class and scripts python files Nov 20, 2012
tpedToVcf.py removed trailing space after INFO in the #header line Mar 12, 2013
variantEvalGenotypeConcordance.py read the gzipped vcf instead Jun 12, 2013
vcf_TwoBitExtract.py added back class and scripts python files Nov 20, 2012
vcf_binQuals.py changed -stop to -end Sep 4, 2013
vcf_callrate.py added back class and scripts python files Nov 20, 2012
vcf_combineVariants-format-compare.py initial commit vcf_combineVariants-format-compare.py May 31, 2013
vcf_extract_set.py Initial commit of vcf_extract_set.py Sep 9, 2013
vcf_extract_variantclass.py added back class and scripts python files Nov 20, 2012
vcf_format-table.py iniital commit vcf_format-table.py Jun 4, 2013
vcf_genotypeSummary.py Accepts either *.vcf.gz or *.vcf files Sep 9, 2013
vcf_gt-filter.py read the gzipped vcf instead Jun 12, 2013
vcf_intersect.py Accept gzipped vcf files as input. Code checks for file extension and… Mar 28, 2014
vcf_mafcut.py added back class and scripts python files Nov 20, 2012
vcf_median_sitedepth.py added back class and scripts python files Nov 20, 2012
vcf_mendel_discrete_filtering.py read a (b)gzip vcf file *.vcf.gz instead Jun 12, 2013
vcf_nrdLog_analysis.py write records to different files depending on how many genotypes are … Apr 21, 2013
vcf_pedigreeSubset.py iniital commit of vcf_pedigreeSubset.py Jan 16, 2014
vcf_pysam_allele_pileup.py read the gzipped vcf instead Jun 12, 2013
vcf_removeSamples.py read the gzipped vcf instead Jun 12, 2013
vcf_toBed4.py added back class and scripts python files Nov 20, 2012
vcf_variantclass_summary.py adjusted regex for parsing info tag Apr 29, 2013

README.md