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- task vcf2bed {
- File vcf
- File vote_file
- String chromo
- String sample_name
- String docker
- String cluster_config
- String disk_size
-
- command <<<
-
- cat ${vcf} | grep -v '#' | grep -v '\./\.' | grep -v '0/0' | cut -f1,2,4,5,10 | sed s'/:/\t/g' | cut -f1-5 > ${sample_name}.${chromo}.all.txt
-
- cat ${vote_file} | awk '{ if (($5 == "./.") ||($5 == "notConsensus")) { print } }' |awk '{ if ($6 != 0) { print } }' > ${chromo}.filtered.txt
-
- cat ${vote_file} | awk '{ if (($5 != "./.") && ($5 != "notConsensus")) { print } }' | grep -v 'CHROM' > ${chromo}.voted.txt
-
- python /opt/split_filtered_voted.py -a ${sample_name}.${chromo}.all.txt -f ${chromo}.filtered.txt -v ${chromo}.voted.txt -p ${sample_name}.${chromo}
-
- >>>
-
- runtime {
- docker:docker
- cluster: cluster_config
- systemDisk: "cloud_ssd 40"
- dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
- }
- output {
- File chromo_filtered_bed = "${sample_name}.${chromo}.filtered.bed"
- File chromo_voted_bed = "${sample_name}.${chromo}.voted.bed"
- }
- }
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