Remove Sites only step from the VAT creation WDL #7510
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rsasch
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| #awk '{print $2}' ~{subpopulation_sample_list} | tail -n +2 | sort -u > collected_subpopulations.txt | ||
| #bcftools query --list-samples ~{local_input_vcf} | sort -u > collected_samples.txt | ||
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| #wc -l collected_subpopulations.txt | ||
| #wc -l collected_samples.txt | ||
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| bcftools view -i 'N_ALT>500 || REF~"N"' ~{local_input_vcf} | bcftools query -f '%CHROM\t%POS\t%ID\t%REF\t%ALT\n' > track_dropped.tsv | ||
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| ## Since Nirvana cant handle N as a base, drop them for now and keep track of the lines dropped | ||
| ## bcftools view -e 'REF~"N"' ~{local_input_vcf} |
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This was referenced Mar 17, 2023
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Move the creation of the sites only vcf into the bcftools step