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Lancet changes to sync with other pipelines #374

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Aug 27, 2020
Merged

Lancet changes to sync with other pipelines #374

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26 changes: 10 additions & 16 deletions modules/somatic/lancet.jst
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Original file line number Diff line number Diff line change
Expand Up @@ -49,23 +49,12 @@
{#
# Lancet sorts output in lexicographical order and this does not
# match the reference fasta order. Here we resort to match the reference
#
# bcftools requires gz or bcf files and we tabix them as a workaround for the improper header given by lancet
#}

bcftools view \
--output-type z \
--output-file "{{ temp_dir }}/{{ loop.index }}.lancet-uns.vcf.gz" \
"{{ temp_dir }}/{{ loop.index }}.lancet-uns.vcf"

bcftools index --tbi --force "{{ temp_dir }}/{{ loop.index }}.lancet-uns.vcf.gz"

bcftools sort \
--max-mem 768M \
--temp-dir {{ temp_dir }}/temp_{{ loop.index }}/ \
--output-type v \
--output-file "{{ temp_dir }}/{{ loop.index }}.lancet.vcf" \
"{{ temp_dir }}/{{ loop.index }}.lancet-uns.vcf.gz"
bcftools reheader \
-f "{{ constants.phoenix.reference_fai }}" \
"{{ temp_dir }}/{{ loop.index }}.lancet-uns.vcf" \
| bcftools sort > "{{ temp_dir }}/{{ loop.index }}.lancet.vcf"

{% endfor %}

Expand Down Expand Up @@ -93,7 +82,7 @@

bcftools concat \
--output-type z \
--output "{{ all_vcf }}" \
--output "{{ temp_dir }}/{{ pair.name }}.{{ aligner }}.lancet.all.uns.vcf.gz" \
{% for b in constants.phoenix.calling_intervals %}
{% if not loop.last %}
"{{ temp_dir }}/{{ loop.index }}.lancet.vcf" \
Expand All @@ -102,6 +91,11 @@
{% endif %}
{% endfor %}

bcftools sort \
--output-type z \
--output-file "{{ all_vcf }}" \
"{{ temp_dir }}/{{ pair.name }}.{{ aligner }}.lancet.all.uns.vcf.gz"

bcftools index --tbi --force "{{ all_vcf }}"

{#
Expand Down