Merge pull request #1613 from lindenb/pl_goleft

added indexcov : finding large INDEL using the BAI index

CHANGELOG.md

@@ -11,6 +11,7 @@ A set of connecting glaciers.
 
 ### Added
 
+- [1613](https://github.com/nf-core/sarek/pull/1613) - add indexcov
 - [1638](https://github.com/nf-core/sarek/pull/1638) - Added additional documentation detailing ASCAT WES usage.
 - [1640](https://github.com/nf-core/sarek/pull/1620) - Add `lofreq` as a tumor-only variant caller
 - [1642](https://github.com/nf-core/sarek/pull/1642) - Back to dev

README.md

@@ -54,6 +54,7 @@ Depending on the options and samples provided, the pipeline can currently perfor
   - `freebayes`
   - `GATK HaplotypeCaller`
   - `Manta`
+  - `indexcov`
   - `mpileup`
   - `MSIsensor-pro`
   - `Mutect2`
@@ -171,6 +172,7 @@ We thank the following people for their extensive assistance in the development
 - [pallolason](https://github.com/pallolason)
 - [Paul Cantalupo](https://github.com/pcantalupo)
 - [Phil Ewels](https://github.com/ewels)
+- [Pierre Lindenbaum](https://github.com/lindenb)
 - [Sabrina Krakau](https://github.com/skrakau)
 - [Sam Minot](https://github.com/sminot)
 - [Sebastian-D](https://github.com/Sebastian-D)

conf/modules/indexcov.config

@@ -0,0 +1,21 @@
+
+// INDEXCOV
+
+process {
+    if (params.tools && params.tools.split(',').contains('indexcov')) {
+
+        withName: 'SAMTOOLS_REINDEX_BAM' {
+            ext.args  = { ' -F 3844 -q 30 ' } // high mapq , primary read paired properly mapped
+        }
+
+        withName: 'GOLEFT_INDEXCOV' {
+            publishDir = [
+                mode: params.publish_dir_mode,
+                path: { "${params.outdir}/variant_calling/indexcov/" }
+                ]
+
+        }
+
+    }
+
+}

docs/output.md

@@ -45,6 +45,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
     - [Strelka](#strelka)
     - [Lofreq](#lofreq)
   - [Structural Variants](#structural-variants)
+    - [Indexcov](#indexcov)
     - [Manta](#manta)
     - [TIDDIT](#tiddit)
   - [Sample heterogeneity, ploidy and CNVs](#sample-heterogeneity-ploidy-and-cnvs)
@@ -592,6 +593,30 @@ For further downstream analysis, take a look [here](https://github.com/Illumina/
 
 ### Structural Variants
 
+#### indexcov
+
+[indexcov](https://github.com/brentp/goleft/tree/master/indexcov) quickly estimate coverage from a whole-genome bam or cram index.
+A bam index has 16KB resolution and it is used as a coverage estimate .
+The output is scaled to around 1. So a long stretch with values of 1.5 would be a heterozygous duplication. This is useful as a quick QC to get coverage values across the genome.
+
+**Output directory: `{outdir}/variantcalling/indexcov/`**
+
+In addition to the interactive HTML files, `indexcov` outputs a number of text files:
+
+- `<sample>-indexcov.ped`: a .ped/.fam file with the inferred sex in the appropriate column if the sex chromosomes were found.
+  the CNX and CNY columns indicating the floating-point estimate of copy-number for those chromosomes.
+  `bins.out`: how many bins had a coverage value outside of (0.85, 1.15). high values can indicate high-bias samples.
+  `bins.lo`: number of bins with value < 0.15. high values indicate missing data.
+  `bins.hi`: number of bins with value > 1.15.
+  `bins.in`: number of bins with value inside of (0.85, 1.15)
+  `p.out`: `bins.out/bins.in`
+  `PC1...PC5`: PCA projections calculated with depth of autosomes.
+
+- `<sample>-indexcov.roc`: tab-delimited columns of chrom, scaled coverage cutoff, and $n_samples columns where each indicates the
+  proportion of 16KB blocks at or above that scaled coverage value.
+- `<sample>-indexcov.bed.gz`: a bed file with columns of chrom, start, end, and a column per sample where the values indicate there
+  scaled coverage for that sample in that 16KB chunk.
+
 #### Manta
 
 [Manta](https://github.com/Illumina/manta) calls structural variants (SVs) and indels from mapped paired-end sequencing reads.

modules.json

@@ -310,6 +310,11 @@
                         "git_sha": "97321eded31a12598837a476d3615300af413bb7",
                         "installed_by": ["modules"]
                     },
+                    "goleft/indexcov": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
                     "lofreq/callparallel": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",

modules/local/samtools/reindex_bam/environment.yml

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::samtools=1.20
+  - bioconda::htslib=1.20

modules/local/samtools/reindex_bam/main.nf

@@ -0,0 +1,57 @@
+/**
+ * The aim of this process is to re-index the bam file without the duplicate, supplementary, unmapped etc, for goleft/indexcov
+ * It creates a BAM containing only a header (so indexcov can get the sample name) and a BAM index were low quality reads, supplementary etc, have been removed
+ */
+process SAMTOOLS_REINDEX_BAM {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' :
+        'biocontainers/samtools:1.20--h50ea8bc_0' }"
+
+    input:
+    tuple val(meta), path(input), path(input_index)
+    tuple val(meta2), path(fasta)
+    tuple val(meta3), path(fai)
+
+    output:
+    tuple val(meta), path("${meta.id}.reindex.bam"), path("${meta.id}.reindex.bam.bai"),emit: output
+    path  "versions.yml"            , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def reference = fasta ? "--reference ${fasta}" : ""
+    """
+    # write header only
+    samtools \\
+        view \\
+        --header-only \\
+        --threads ${task.cpus} \\
+        -O BAM \\
+        -o "${meta.id}.reindex.bam" \\
+        ${reference} \\
+        ${input}
+
+    # write BAM index only, remove unmapped, supplementary, etc...
+    samtools \\
+        view \\
+        --uncompressed \\
+        --write-index \\
+        --threads ${task.cpus} \\
+        -O BAM \\
+        -o "/dev/null##idx##${meta.id}.reindex.bam.bai" \\
+        ${reference} \\
+        ${args} \\
+        ${input}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
+}