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Merge pull request #4 from tgen/phoenix-sync
Coyote v1.2.1
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| Original file line number | Diff line number | Diff line change |
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| {% macro expansion_hunter(sample, aligner='bwa') %} | ||
| {% set bam %}{{ sample.gltype }}/alignment/{{ aligner }}/{{ sample.name }}/{{ sample.name }}.{{ aligner }}.bam{% endset %} | ||
| {% set temp_dir %}temp/{{ sample.gltype }}/constitutional_variant_calls/expansion_hunter/{{ sample.name }}{% endset %} | ||
| {% set results_dir %}{{ sample.gltype }}/constitutional_variant_calls/expansion_hunter/{{ sample.name }}{% endset %} | ||
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| - name: expansion_hunter_{{ aligner }}_{{ sample.name }}_{{ aligner }} | ||
| tags: [{{ sample.gltype }}, repeats, expansion, SRT, {{ sample.name }}] | ||
| input: {{ bam }} | ||
| output: | ||
| - {{ results_dir }}/{{ sample.name }}.expansion_hunter.all.vcf.gz | ||
| - {{ results_dir }}/{{ sample.name }}.expansion_hunter.all.vcf.gz.tbi | ||
| walltime: "24:00:00" | ||
| cpus: 1 | ||
| mem: 2G | ||
| cmd: | | ||
| set -eu | ||
| set -o pipefail | ||
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| module load {{ constants.tools.expansion_hunter.module }} | ||
| module load {{ constants.tools.bcftools.module }} | ||
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| rm -r {{ temp_dir }} || true | ||
| mkdir -p {{ temp_dir }} | ||
| mkdir -p {{ results_dir }} | ||
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| {# The variant catalog is in the install path, we grab the path here #} | ||
| {# ExpansionHunter is in a /bin directory, we want to go one level higher #} | ||
| eh_path=$(dirname $(dirname `which ExpansionHunter`)) | ||
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| ExpansionHunter \ | ||
| --reads {{ bam }} \ | ||
| --reference {{ constants.coyote.reference_fasta }} \ | ||
| --variant-catalog ${eh_path}/variant_catalog/grch38/variant_catalog.json \ | ||
| --output-prefix {{ temp_dir }}/{{ sample.name }}.expansion_hunter | ||
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| bcftools view \ | ||
| --output-type z \ | ||
| --output-file {{ results_dir }}/{{ sample.name }}.expansion_hunter.all.vcf.gz \ | ||
| {{ temp_dir }}/{{ sample.name }}.expansion_hunter.vcf | ||
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| bcftools index --tbi --force {{ results_dir }}/{{ sample.name }}.expansion_hunter.all.vcf.gz | ||
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| - name: expansion_hunter_filter_variants_{{ sample.name }}_{{ aligner }} | ||
| tags: [{{ sample.gltype}}, constitutional, snp_indel_caller, deepvariant, {{ sample.name }}] | ||
| input: | ||
| - {{ results_dir }}/{{ sample.name }}.expansion_hunter.all.vcf.gz | ||
| - {{ results_dir }}/{{ sample.name }}.expansion_hunter.all.vcf.gz.tbi | ||
| output: | ||
| - {{ results_dir }}/{{ sample.name }}.expansion_hunter.pass.vcf.gz | ||
| - {{ results_dir }}/{{ sample.name }}.expansion_hunter.pass.vcf.gz.tbi | ||
| cpus: 1 | ||
| mem: 2G | ||
| walltime: "12:00:00" | ||
| cmd: | | ||
| set -eu | ||
| set -o pipefail | ||
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| module load {{ constants.tools.bcftools.module }} | ||
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| {# Then filter out the PASS variants to a separate file #} | ||
| bcftools filter \ | ||
| --output-type z \ | ||
| --include 'FILTER == "PASS"' \ | ||
| {% if sample.gltype == 'exome' %} | ||
| --targets-file "{{ sample.capture_kit.extended_bed }}" \ | ||
| {% endif %} | ||
| "{{ results_dir }}/{{ sample.name }}.expansion_hunter.all.vcf.gz" \ | ||
| > "{{ results_dir }}/{{ sample.name }}.expansion_hunter.pass.vcf.gz" | ||
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| bcftools index --tbi --force "{{ results_dir }}/{{ sample.name }}.expansion_hunter.pass.vcf.gz" | ||
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| {% endmacro %} |
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