LUYAO REN
4 lat temu
1 zmienionych plików z 2 dodań i 2 usunięć
+ 2
- 2
tasks/region.wdl
Wyświetl plik
| for i in *vcf.gz | for i in *vcf.gz | ||||
| do | do | ||||
| zcat $i | grep -v '#' | grep 'SNV' >> ${sample_name}.${tag}.all.snv.count.txt | |||||
| zcat $i | grep -v '#' | grep 'INDEL' >> ${sample_name}.${tag}.all.indel.count.txt | |||||
| zcat $i | grep -v '#' | grep 'SNV' | wc -l >> ${sample_name}.${tag}.all.snv.count.txt | |||||
| zcat $i | grep -v '#' | grep 'INDEL'| wc -l >> ${sample_name}.${tag}.all.indel.count.txt | |||||
| zcat $i | grep -v '#' | grep 'SNV;MC' | wc -l >> ${sample_name}.${tag}.snv.mc.count.txt | zcat $i | grep -v '#' | grep 'SNV;MC' | wc -l >> ${sample_name}.${tag}.snv.mc.count.txt | ||||
| zcat $i | grep -v '#' | grep 'SNV;MC' | awk '{ if (($10 == $11) && ($11 == $12) && ($12 == $13)) { print } }' | wc -l >> ${sample_name}.${tag}.snv.mc.same.genotype.count.txt | zcat $i | grep -v '#' | grep 'SNV;MC' | awk '{ if (($10 == $11) && ($11 == $12) && ($12 == $13)) { print } }' | wc -l >> ${sample_name}.${tag}.snv.mc.same.genotype.count.txt | ||||
| zcat $i | grep -v '#' | grep 'INDEL;MC' | wc -l >> ${sample_name}.${tag}.indel.mc.count.txt | zcat $i | grep -v '#' | grep 'INDEL;MC' | wc -l >> ${sample_name}.${tag}.indel.mc.count.txt |
Ładowanie…