Mercurial > repos > stef > falco
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author | stef |
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date | Wed, 25 Feb 2015 08:50:56 -0500 |
parents | a793ffd0cd04 |
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Usage: falco input: - bam file - manifest file - ref + fai - locifilt - manifest output: - *.vcf file - *.qc.ann.txt -> catalog of each assayed bp - *.qc2.ann.txt -> catalog of transitions - *.qc.targets.txt -> amplicon centered information, eg depth, start/end positions. example: OUTBASE="HCT116-TEST" ## variant calling falco --bam data/HCT-116/HCT116.bam --output $OUTBASE --ref genome.fa file1=$OUTBASE".qc.ann.qual.txt" file2=$OUTBASE".qc2.ann.txt" file3=$OUTBASE".qc.targets.txt" file4=$OUTBASE".res.filtered.tsv" ## variant filtering and reporting falco-filter-report --vcf snpeff.vcf --output $OUTBASE --qc_ann_qual_txt $file1 --qc2_ann_txt $file2 --qc_targets_txt $file3 --res_filtered_tsv $file4