From 5729d2d5318679bb52c79e306700487df5b91399 Mon Sep 17 00:00:00 2001 From: Jacki Novik Date: Tue, 18 Jul 2017 00:18:51 +0000 Subject: [PATCH] hacky way to read in variant stats when filetype unknown - related to issue #228 --- variant_stats.py | 227 +++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 227 insertions(+) create mode 100644 variant_stats.py diff --git a/variant_stats.py b/variant_stats.py new file mode 100644 index 0000000..d854efc --- /dev/null +++ b/variant_stats.py @@ -0,0 +1,227 @@ +# Copyright (c) 2017. Mount Sinai School of Medicine +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +from collections import namedtuple + +VariantStats = namedtuple("VariantStats", + ["depth", "alt_depth", "variant_allele_frequency"]) +SomaticVariantStats = namedtuple("SomaticVariantStats", + ["tumor_stats", "normal_stats"]) + +def strelka_somatic_variant_stats(variant, variant_metadata): + """Parse out the variant calling statistics for a given variant from a Strelka VCF + + Parameters + ---------- + variant : varcode.Variant + sample_info : dict + Dictionary of sample to variant calling statistics, corresponds to the sample columns + in a Strelka VCF + + Returns + ------- + SomaticVariantStats + """ + + sample_info = variant_metadata["sample_info"] + # Ensure there are exactly two samples in the VCF, a tumor and normal + assert len(sample_info) == 2, "More than two samples found in the somatic VCF" + tumor_stats = _strelka_variant_stats(variant, sample_info["TUMOR"]) + normal_stats = _strelka_variant_stats(variant, sample_info["NORMAL"]) + return SomaticVariantStats(tumor_stats=tumor_stats, normal_stats=normal_stats) + +def _strelka_variant_stats(variant, sample_info): + """Parse a single sample"s variant calling statistics based on Strelka VCF output + + Parameters + ---------- + variant : varcode.Variant + sample_info : dict + Dictionary of Strelka-specific variant calling fields + + Returns + ------- + VariantStats + """ + + if variant.is_deletion or variant.is_insertion: + # ref: https://sites.google.com/site/strelkasomaticvariantcaller/home/somatic-variant-output + ref_depth = int(sample_info['TAR'][0]) # number of reads supporting ref allele (non-deletion) + alt_depth = int(sample_info['TIR'][0]) # number of reads supporting alt allele (deletion) + depth = ref_depth + alt_depth + else: + # Retrieve the Tier 1 counts from Strelka + ref_depth = int(sample_info[variant.ref+"U"][0]) + alt_depth = int(sample_info[variant.alt+"U"][0]) + depth = alt_depth + ref_depth + if depth > 0: + vaf = float(alt_depth) / depth + else: + # unclear how to define vaf if no reads support variant + # up to user to interpret this (hopefully filtered out in QC settings) + vaf = None + + return VariantStats(depth=depth, alt_depth=alt_depth, variant_allele_frequency=vaf) + +def mutect_somatic_variant_stats(variant, variant_metadata): + """Parse out the variant calling statistics for a given variant from a Mutect VCF + + Parameters + ---------- + variant : varcode.Variant + sample_info : dict + Dictionary of sample to variant calling statistics, corresponds to the sample columns + in a Mutect VCF + + Returns + ------- + SomaticVariantStats + """ + + sample_info = variant_metadata["sample_info"] + # Ensure there are exactly two samples in the VCF, a tumor and normal + assert len(sample_info) == 2, "More than two samples found in the somatic VCF" + + # Find the sample with the genotype field set to variant in the VCF + tumor_sample_infos = [info for info in sample_info.values() if info["GT"] == "0/1"] + + # Ensure there is only one such sample + assert len(tumor_sample_infos) == 1, "More than one tumor sample found in the VCF file" + + tumor_sample_info = tumor_sample_infos[0] + normal_sample_info = [info for info in sample_info.values() if info["GT"] != "0/1"][0] + + tumor_stats = _mutect_variant_stats(variant, tumor_sample_info) + normal_stats = _mutect_variant_stats(variant, normal_sample_info) + return SomaticVariantStats(tumor_stats=tumor_stats, normal_stats=normal_stats) + +def _mutect_variant_stats(variant, sample_info): + """Parse a single sample"s variant calling statistics based on Mutect"s (v1) VCF output + + Parameters + ---------- + variant : varcode.Variant + sample_info : dict + Dictionary of Mutect-specific variant calling fields + + Returns + ------- + VariantStats + """ + + # Parse out the AD (or allele depth field), which is an array of [REF_DEPTH, ALT_DEPTH] + ref_depth, alt_depth = sample_info["AD"] + depth = int(ref_depth) + int(alt_depth) + vaf = float(alt_depth) / depth + + return VariantStats(depth=depth, alt_depth=alt_depth, variant_allele_frequency=vaf) + +def _maf_variant_stats(variant, variant_metadata, prefix="t"): + ref_depth = variant_metadata["%s_ref_count" % prefix] + alt_depth = variant_metadata["%s_alt_count" % prefix] + depth = int(ref_depth) + int(alt_depth) + vaf = float(alt_depth) / depth + return VariantStats(depth=depth, alt_depth=alt_depth, variant_allele_frequency=vaf) + +def maf_somatic_variant_stats(variant, variant_metadata): + """ + Parse out the variant calling statistics for a given variant from a MAF file + + Assumes the MAF format described here: https://www.biostars.org/p/161298/#161777 + + Parameters + ---------- + variant : varcode.Variant + variant_metadata : dict + Dictionary of metadata for this variant + + Returns + ------- + SomaticVariantStats + """ + tumor_stats = None + normal_stats = None + if "t_ref_count" in variant_metadata: + tumor_stats = _maf_variant_stats(variant, variant_metadata, prefix="t") + if "n_ref_count" in variant_metadata: + normal_stats = _maf_variant_stats(variant, variant_metadata, prefix="n") + return SomaticVariantStats(tumor_stats=tumor_stats, normal_stats=normal_stats) + +def _vcf_is_strelka(variant_file): + """Return True if variant_file given is in strelka format + """ + if "strelka" in variant_file.lower(): + return True + return False + +def _vcf_is_maf(variant_file): + """Retrun True if variant_file given is in .maf format + """ + if ".maf" in variant_file.lower(): + return True + return False + +def _vcf_is_mutect(variant_file): + """Return True if variant_file give is in mutect format + """ + if "mutect" in variant_file.lower(): + return True + else: + try: + vcf_reader = vcf.Reader(open(variant_file, "r")) + if vcf_reader.metadata["GATKCommandLine"][0]["ID"] == "MuTect": + return True + except: + pass + return False + +def variant_stats_from_variant(variant, + metadata, + merge_fn=(lambda all_stats: \ + max(all_stats, key=(lambda stats: stats.tumor_stats.depth)))): + """Parse the variant calling stats from a variant called from multiple variant files. The stats are merged + based on `merge_fn` + + Parameters + ---------- + variant : varcode.Variant + metadata : dict + Dictionary of variant file to variant calling metadata from that file + merge_fn : function + Function from list of SomaticVariantStats to single SomaticVariantStats. + This is used if a variant is called by multiple callers or appears in multiple VCFs. + By default, this uses the data from the caller that had a higher tumor depth. + + Returns + ------- + SomaticVariantStats + """ + all_stats = [] + for (variant_file, variant_metadata) in metadata.items(): + if _vcf_is_maf(variant_file=variant_file): + stats = maf_somatic_variant_stats(variant, variant_metadata) + elif _vcf_is_strelka(variant_file=variant_file): + stats = strelka_somatic_variant_stats(variant, variant_metadata) + elif _vcf_is_mutect(variant_file=variant_file): + stats = mutect_somatic_variant_stats(variant, variant_metadata) + else: + try: + stats = strelka_somatic_variant_stats(variant, variant_metadata) + except: + try: + stats = mutect_somatic_variant_stats(variant, variant_metadata) + except: + raise ValueError("Cannot parse sample fields, variant file {} is from an unsupported caller.".format(variant_file)) + all_stats.append(stats) + return merge_fn(all_stats)