Sentieon Tools for Alignment and Variant Analysis

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sentieon tools

:speech_balloon: Introduction

The module consists of tools from Sentieon, including alignment, duplicate reads removal, indel realignment, recalibration table calculation and DNAScope and TNScope SNV/structural variants

Code Snippets

shell:
    "{params.sentieon} bwa mem "
    "-M -R '@RG\\tID:{wildcards.sample}_{wildcards.type}\\tSM:{wildcards.sample}_{wildcards.type}\\tPL:ILLUMINA' "
    "-t {threads} {params.reference} {input.reads} "
    "| {params.sentieon} util sort -o {output.bam} "
    "-t {threads} "
    "--sam2bam "
    "-i - &> {log}"

SnakeMake BWA From line 35 of rules/sentieon.smk

shell:
    "{params.sentieon} driver "
    "-t {threads} "
    "-i {input} "
    "--algo LocusCollector "
    "--fun score_info "
    "sentieon/dedup/{wildcards.sample}_{wildcards.type}_DEDUP_score.txt ; "
    "{params.sentieon} driver "
    "-t {threads} "
    "-i {input} "
    "--algo Dedup "
    "--rmdup "
    "--score_info sentieon/dedup/{wildcards.sample}_{wildcards.type}_DEDUP_score.txt "
    "--metrics sentieon/dedup/{wildcards.sample}_{wildcards.type}_DEDUP.txt "
    "sentieon/dedup/{wildcards.sample}_{wildcards.type}_DEDUP.bam &> {log}"

SnakeMake From line 73 of rules/sentieon.smk

shell:
    "{params.sentieon} driver "
    "-t {threads} "
    "-r {params.reference} "
    "-i {input.bam} "
    "--algo Realigner "
    "-k {params.mills} {output.bam} &> {log}"

SnakeMake From line 117 of rules/sentieon.smk

shell:
    "{params.sentieon} driver "
    "-t {threads} "
    "-r {params.reference} "
    "-i {input.bam} "
    "--algo QualCal "
    "-k {params.mills} "
    "-k {params.dbsnp} {output} &> {log}"

SnakeMake From line 152 of rules/sentieon.smk

shell:
    "{params.sentieon} driver "
    "-t {threads} "
    "-r {params.reference} "
    "-i {input.bam} "
    "--algo DNAscope "
    "-d {params.dbsnp} "
    "--var_type snp,indel "
    "--model {params.model} {params.callsettings} {output.dnascope_vcf} &> {log}"

SnakeMake From line 190 of rules/sentieon.smk

shell:
    "{params.sentieon} driver -t {threads} "
    "-r {params.reference} "
    "--algo DNAModelApply "
    "--model {params.model} "
    "-v {input.vcf} {output.vcf} &> {log}"

SnakeMake From line 231 of rules/sentieon.smk

shell:
    "{params.sentieon} driver "
    "-t {threads} "
    "-r {params.reference} "
    "-i {input.tumorbam} "
    "-q {input.tumortable} "
    "-i {input.normalbam} "
    "-q {input.normaltable} "
    "--algo TNscope "
    "--tumor_sample {wildcards.sample}_T "
    "--normal_sample {wildcards.sample}_N "
    "--bam_output {output.tnscope_bam} "
    "{params.callsettings} {output.tnscope} &> {log}"

SnakeMake From line 268 of rules/sentieon.smk

shell:
    "{params.sentieon} driver "
    "-t {threads} "
    "-r {params.reference} "
    "--algo TNModelApply "
    "-m {params.model} "
    "-v {input.tnscopevcf} {output.vcf} &> {log}"