From 2ecc73fa4c54773ede8325316f2117d70d3a507e Mon Sep 17 00:00:00 2001
From: Tobias Marschall <tobias.marschall@0ohm.net>
Date: Fri, 6 Jul 2018 16:15:53 +0200
Subject: [PATCH] Added rules to re-genotype a set of given SNVs (e.g. from
1000G) and to do haplotagging of BAM files. Slightly reorganized input file
structure: now expect two separate folders "bam/{sample}/selected" and
"bam/{sample}/all", where "selected" should contain the good Strand-seq
libraries, where all should contain all libraries that can be used for SNV
calling/genotyping.
---
Snake.config.json | 2 +
Snakefile | 99 +++++++++++++++++++++++++++++++++++++----------
2 files changed, 80 insertions(+), 21 deletions(-)
diff --git a/Snake.config.json b/Snake.config.json
index 930151e..ba5b671 100644
--- a/Snake.config.json
+++ b/Snake.config.json
@@ -15,6 +15,8 @@
"RPE1-WT" : "/g/korbel2/StrandSeq/20180606_RPE1-WT/regenSNVs_GRCh38sites_RPEWTstrandS_chr1-22plusX.filtered.vcf.gz"
},
+ "snv_sites_to_genotype": "",
+
"variable_bins" : {
"50000" : "utils/variable_bins.GRCh38.50kb.bed",
"100000" : "utils/variable_bins.GRCh38.100kb.bed"
diff --git a/Snakefile b/Snakefile
index c45d8c7..7de24b8 100644
--- a/Snakefile
+++ b/Snakefile
@@ -1,14 +1,24 @@
import math
+from collections import defaultdict
configfile: "Snake.config.json"
-SAMPLE,BAM = glob_wildcards("bam/{sample}/{bam}.bam")
-BAM_PER_SAMPLE = dict([(s,[]) for s in SAMPLE])
-for i in range(len(SAMPLE)):
- BAM_PER_SAMPLE[SAMPLE[i]].append(BAM[i])
-print("Detected {} samples:".format(len(set(SAMPLE))))
-for s in set(SAMPLE):
- print(" {}:\t{} cells".format(s, len(BAM_PER_SAMPLE[s])))
+SAMPLE,BAM = glob_wildcards("bam/{sample}/selected/{bam}.bam")
+SAMPLES = sorted(set(SAMPLE))
+
+BAM_PER_SAMPLE = defaultdict(list)
+for sample,bam in zip(SAMPLE,BAM):
+ BAM_PER_SAMPLE[sample].append(bam)
+
+ALLBAMS_PER_SAMPLE = defaultdict(list)
+for sample in SAMPLES:
+ ALLBAMS_PER_SAMPLE[sample] = glob_wildcards("bam/{}/all/{{bam}}.bam".format(sample)).bam
+
+print("Detected {} samples:".format(len(SAMPLES)))
+for s in SAMPLES:
+ print(" {}:\t{} cells\t {} selected cells".format(s, len(ALLBAMS_PER_SAMPLE[s]), len(BAM_PER_SAMPLE[s])))
+
+
import os.path
@@ -41,21 +51,22 @@ localrules:
rule all:
input:
- expand("plots/{sample}/{window}_fixed.pdf", sample = SAMPLE, window = [50000, 100000, 200000, 500000]),
- expand("plots/{sample}/{window}_fixed_norm.pdf", sample = SAMPLE, window = [50000, 100000, 200000]),
+ expand("plots/{sample}/{window}_fixed.pdf", sample = SAMPLES, window = [50000, 100000, 200000, 500000]),
+ expand("plots/{sample}/{window}_fixed_norm.pdf", sample = SAMPLES, window = [50000, 100000, 200000]),
expand("sv_calls/{sample}/{window}_fixed_norm.{bpdens}/plots/sv_calls/{method}.{chrom}.pdf",
sample = SAMPLE,
chrom = config["chromosomes"],
window = [50000, 100000],
bpdens = ["few","medium","many"],
method = METHODS),
- expand("ploidy/{sample}/ploidy.{chrom}.txt", sample = SAMPLE, chrom = config["chromosomes"]),
+ expand("ploidy/{sample}/ploidy.{chrom}.txt", sample = SAMPLES, chrom = config["chromosomes"]),
expand("sv_calls/{sample}/{window}_fixed_norm.{bpdens}/plots/sv_consistency/{method}.consistency-barplot-{af}.pdf",
- sample = SAMPLE,
+ sample = SAMPLES,
window = [50000, 100000],
bpdens = ["few","medium","many"],
method = METHODS,
af = ["high","med","low","rare"]),
+ ['haplotag/bam/{}/{}.bam'.format(sample,bam) for bam in BAM_PER_SAMPLE[sample] for sample in SAMPLES],
################################################################################
@@ -288,7 +299,7 @@ rule generate_exclude_file_1:
output:
temp("log/exclude_file.temp")
input:
- bam = expand("bam/{sample}/{bam}.bam", sample = SAMPLE[0], bam = BAM[0])
+ bam = expand("bam/{sample}/selected/{bam}.bam", sample = SAMPLES[0], bam = ALLBAMS_PER_SAMPLE[SAMPLES[0]][0])
log:
"log/generate_exclude_file_1.log"
params:
@@ -317,8 +328,8 @@ rule generate_exclude_file_2:
rule mosaic_count_fixed:
input:
- bam = lambda wc: expand("bam/" + wc.sample + "/{bam}.bam", bam = BAM_PER_SAMPLE[wc.sample]) if wc.sample in BAM_PER_SAMPLE else "FOOBAR",
- bai = lambda wc: expand("bam/" + wc.sample + "/{bam}.bam.bai", bam = BAM_PER_SAMPLE[wc.sample]) if wc.sample in BAM_PER_SAMPLE else "FOOBAR",
+ bam = lambda wc: expand("bam/" + wc.sample + "/selected/{bam}.bam", bam = BAM_PER_SAMPLE[wc.sample]) if wc.sample in BAM_PER_SAMPLE else "FOOBAR",
+ bai = lambda wc: expand("bam/" + wc.sample + "/selected/{bam}.bam.bai", bam = BAM_PER_SAMPLE[wc.sample]) if wc.sample in BAM_PER_SAMPLE else "FOOBAR",
excl = "log/exclude_file"
output:
counts = "counts/{sample}/{window}_fixed.txt.gz",
@@ -342,8 +353,8 @@ rule mosaic_count_fixed:
rule mosaic_count_variable:
input:
- bam = lambda wc: expand("bam/" + wc.sample + "/{bam}.bam", bam = BAM_PER_SAMPLE[wc.sample]),
- bai = lambda wc: expand("bam/" + wc.sample + "/{bam}.bam.bai", bam = BAM_PER_SAMPLE[wc.sample]),
+ bam = lambda wc: expand("bam/" + wc.sample + "/selected/{bam}.bam", bam = BAM_PER_SAMPLE[wc.sample]),
+ bai = lambda wc: expand("bam/" + wc.sample + "/selected/{bam}.bam.bai", bam = BAM_PER_SAMPLE[wc.sample]),
bed = lambda wc: config["variable_bins"][str(wc.window)],
excl = "log/exclude_file"
output:
@@ -567,7 +578,10 @@ rule prepare_strandphaser_config_per_chrom:
def locate_snv_vcf(wildcards):
if "snv_calls" not in config or wildcards.sample not in config["snv_calls"] or config["snv_calls"][wildcards.sample] == "":
- return "snv_calls/{}/{}.vcf".format(wildcards.sample, wildcards.chrom)
+ if "snv_sites_to_genotype" in config and config["snv_sites_to_genotype"] != "":
+ return "snv_genotyping/{}/{}.vcf".format(wildcards.sample, wildcards.chrom)
+ else:
+ return "snv_calls/{}/{}.vcf".format(wildcards.sample, wildcards.chrom)
else:
return "external_snv_calls/{}/{}.vcf".format(wildcards.sample, wildcards.chrom)
@@ -577,9 +591,10 @@ rule run_strandphaser_per_chrom:
snppositions = locate_snv_vcf,
configfile = "strand_states/{sample}/StrandPhaseR.{chrom}.config",
strandphaser = "utils/R-packages/StrandPhaseR/R/StrandPhaseR",
- bamfolder = "bam/{sample}/"
+ bamfolder = "bam/{sample}/selected"
output:
- "strand_states/{sample}/StrandPhaseR_analysis.{chrom}/Phased/phased_haps.txt"
+ "strand_states/{sample}/StrandPhaseR_analysis.{chrom}/Phased/phased_haps.txt",
+ "strand_states/{sample}/StrandPhaseR_analysis.{chrom}/VCFfiles/{chrom}_phased.vcf",
log:
"log/run_strandphaser_per_chrom/{sample}/{chrom}.log"
shell:
@@ -594,6 +609,16 @@ rule run_strandphaser_per_chrom:
> {log} 2>&1
"""
+rule merge_strandphaser_vcfs:
+ input:
+ vcf=expand("strand_states/{{sample}}/StrandPhaseR_analysis.{chrom}/VCFfiles/{chrom}_phased.vcf", chrom=config["chromosomes"])
+ output:
+ vcf='phased-snvs/{sample}.vcf.gz'
+ log:
+ "log/merge_strandphaser_vcfs/{sample}.log"
+ shell:
+ "(bcftools concat -a | bcftools view -o {output.vcf} -O z --genotype het --types snps - ) > {log} 2>&1"
+
rule combine_strandphaser_output:
@@ -625,6 +650,21 @@ rule convert_strandphaser_output:
"utils/helper.convert_strandphaser_output.R"
+################################################################################
+# Haplotagging #
+################################################################################
+
+rule haplotag_bams:
+ input:
+ vcf='phased-snvs/{sample}.vcf.gz',
+ bam='bam/{sample}/selected/{bam}.bam',
+ ref = config["reference"],
+ output:
+ bam='haplotag/bam/{sample}/{bam}.bam',
+ log:
+ "log/haplotag_bams/{sample}.log"
+ shell:
+ "whatshap haplotag -o {output.bam} -r {input.ref} {input.vcf} {input.bam} > {log} 2>{log}"
################################################################################
# Call SNVs #
@@ -632,7 +672,7 @@ rule convert_strandphaser_output:
rule mergeBams:
input:
- lambda wc: expand("bam/" + wc.sample + "/{bam}.bam", bam = BAM_PER_SAMPLE[wc.sample]) if wc.sample in BAM_PER_SAMPLE else "FOOBAR",
+ lambda wc: expand("bam/" + wc.sample + "/all/{bam}.bam", bam = ALLBAMS_PER_SAMPLE[wc.sample]) if wc.sample in ALLBAMS_PER_SAMPLE else "FOOBAR",
output:
"snv_calls/{sample}/merged.bam"
log:
@@ -657,7 +697,7 @@ rule call_SNVs_bcftools_chrom:
bam = "snv_calls/{sample}/merged.bam",
bai = "snv_calls/{sample}/merged.bam.bai"
output:
- "snv_calls/{sample}/{chrom}.vcf"
+ "snv_calls/{sample}/{chrom,chr[0-9A-Z]+}.vcf"
log:
"log/call_SNVs_bcftools_chrom/{sample}/{chrom}.log"
params:
@@ -670,6 +710,23 @@ rule call_SNVs_bcftools_chrom:
| {params.bcftools} call -mv - | {params.bcftools} view --genotype het --types snps - > {output} 2> {log}
"""
+rule regenotype_SNVs:
+ input:
+ bam = "snv_calls/{sample}/merged.bam",
+ bai = "snv_calls/{sample}/merged.bam.bai",
+ fa = config["reference"],
+ sites = config["snv_sites_to_genotype"],
+ output:
+ vcf = "snv_genotyping/{sample}/{chrom,chr[0-9A-Z]+}.vcf"
+ log:
+ "log/snv_genotyping/{sample}/{chrom}.log"
+ params:
+ bcftools = config["bcftools"]
+ shell:
+ """
+ (freebayes -f {input.fa} -r {wildcards.chrom} -@ {input.sites} --only-use-input-alleles {input.bam} --genotype-qualities | {params.bcftools} view --exclude-uncalled --genotype het --types snps --include "QUAL>=10" - > {output.vcf}) 2> {log}
+ """
+
rule merge_SNV_calls:
input:
expand("snv_calls/{{sample}}/{chrom}.vcf", chrom = config['chromosomes'])
--
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