Output Files¶
This table summarises the locations of important output files.
Path | Notes |
bams/final_bams/{sample}.bam[$|.bai] | |
germline/VCF/{sample}.germline.vcf.gz[$|.tbi] | |
{mode}/SNP_Indels/*/vcf/{sample}.norm.vcf.gz* | The first wildcard captures any/all variant callers; the second one will also include the index file (vcf.gz.tbi) |
{mode}/SNP_Indels/*/cohort_summary/all_somatic_variants.maf | Contains minimally filtered variants from all samples |
{mode}/ffpe_filter/sobdetector/*/pass2/{sample}.artifact_filtered.vcf.gz* | Only exists if FFPE filter is turned on |
{mode}/ffpe_filter/sobdetector/*/cohort_summary/all_somatic_variants.maf | |
{mode}/CNV/freec_out/pass2/{sample}.recal.bam_CNVs.p.value.txt | Only exists if CNV calling is turned on and run in paired mode; `{mode}` can only be "somatic_paired" |
{mode}/CNV/freec_out/pass1/{sample}.recal.bam_CNVs.p.value.txt | |
{mode}/CNV/sequenza_out/{sample}_alternative_solutions.txt | |
{mode}/CNV/sequenza_out/{sample}/seqz_segments.txt | |
QC/MultiQC_Report.html | |
QC/MultiQC_Report_data/ | (Optional?) |
Please Note:
{sample}is the sample ID derived from original fastq (i.e.{sample}.R1.fastq.gz) OR bam (i.e.{sample}.bam), and{mode}will be somatic_paired or somatic_tumor_only depending on whether tumor-normal pairs were provided.