From 16f01d2fd2e1da9ad21fe133f4f6b79c5d4dbf0e Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Mon, 8 Oct 2018 21:11:34 +0200
Subject: [PATCH] SNP_calling.nf: fix format
---
src/SNP_calling.config | 4 ++--
src/SNP_calling.nf | 14 ++++++++------
2 files changed, 10 insertions(+), 8 deletions(-)
diff --git a/src/SNP_calling.config b/src/SNP_calling.config
index 1f8c667..34660e0 100644
--- a/src/SNP_calling.config
+++ b/src/SNP_calling.config
@@ -34,10 +34,10 @@ profiles {
container = "samtools:1.7"
}
withName: samtools_SNP_tumor {
- container = "samtools:1.7"
+ container = "bcftools:1.7"
}
withName: samtools_SNP_norm {
- container = "samtools:1.7"
+ container = "bcftools:1.7"
}
withName: vcf_to_csv_tumor {
container = "gatk:4.0.8.1"
diff --git a/src/SNP_calling.nf b/src/SNP_calling.nf
index 0de5eb4..2c9cdfc 100644
--- a/src/SNP_calling.nf
+++ b/src/SNP_calling.nf
@@ -355,7 +355,8 @@ process samtools_SNP_tumor {
script:
"""
-samtools mpileup -AE -uf ${fasta} ${bam_tumor} | \
+bcftools mpileup -AE -f ${fasta} ${bam_tumor} --output-type v \
+-a FORMAT/AD,FORMAT/ADF,FORMAT/ADR,FORMAT/DP,FORMAT/SP,INFO/AD,INFO/ADF,INFO/ADR | \
bcftools call -mv --output-type v > ${file_id_tumor}_raw.vcf
bcftools filter -s LowQual -e '%QUAL<20 || DP>100' ${file_id_tumor}_raw.vcf \
> ${file_id_tumor}_filtered.vcf
@@ -379,7 +380,8 @@ process samtools_SNP_norm {
script:
"""
-samtools mpileup -AE -uf ${fasta} ${bam_norm} | \
+bcftools mpileup -AE -f ${fasta} ${bam_norm} --output-type v \
+-a FORMAT/AD,FORMAT/ADF,FORMAT/ADR,FORMAT/DP,FORMAT/SP,INFO/AD,INFO/ADF,INFO/ADR | \
bcftools call -mv --output-type v > ${file_id_norm}_raw.vcf
bcftools filter -s LowQual -e '%QUAL<20 || DP>100' ${file_id_norm}_raw.vcf \
> ${file_id_norm}_filtered.vcf
@@ -400,10 +402,10 @@ process vcf_to_csv_tumor {
script:
"""
gatk VariantsToTable -V ${file_id_tumor}_raw.vcf \
--F CHROM -F POS -F TYPE -GF GT -GF AD -GF AF \
+-F CHROM -F POS -F TYPE -GF GT -GF AD -F AD -F DP \
-O ${file_id_tumor}_raw.csv
gatk VariantsToTable -V ${file_id_tumor}_filtered.vcf \
--F CHROM -F POS -F TYPE -GF GT -GF AD -GF AF \
+-F CHROM -F POS -F TYPE -GF GT -GF AD -F AD -F DP \
-O ${file_id_tumor}_filtered.csv
"""
}
@@ -422,10 +424,10 @@ process vcf_to_csv_norm {
script:
"""
gatk VariantsToTable -V ${file_id_norm}_raw.vcf \
--F CHROM -F POS -F TYPE -GF GT -GF AD -GF AF \
+-F CHROM -F POS -F TYPE -GF GT -GF AD -F AD -F DP \
-O ${file_id_norm}_raw.csv
gatk VariantsToTable -V ${file_id_norm}_filtered.vcf \
--F CHROM -F POS -F TYPE -GF GT -GF AD -GF AF \
+-F CHROM -F POS -F TYPE -GF GT -GF AD -F AD -F DP \
-O ${file_id_norm}_filtered.csv
"""
}
--
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