The following should be allowable inputs:
- Valid VCF. Should accept both a full VCF (9 cols + samples) and a genotype free VCF with just the 8 columns
| COLUMN | Description |
|---|---|
| 1 | #CHROM |
| 2 | POS |
| 3 | ID |
| 4 | REF |
| 5 | ALT |
| 6 | QUAL |
| 7 | FILTER |
| 8 | INFO |
- TCGA MAF (see TCGA spec)
A fully formed valid VCF file with the following FORMAT fields:
| FIELD | Description |
|---|---|
| DP | Total depth |
| RD | Depth matching reference (REF) allele |
| AD | Depth matching alternate (ALT) allele |
| VF | Variant frequency (AD/DP) |
| DPP | Depth on postitive strand |
| DPN | Depth on negative strand |
| RDP | Reference depth on postitive strand |
| RDN | Reference depth on negative strand |
| ADP | Alternate depth on postitive strand |
| ADN | Alternate depth on negative strand |
Use the following default filters for the Phase I tests:
- MAPQ >= 20
- BASEQ >= 0
- Count improper pair (proper pair filter OFF)
- Do not count duplicates (duplicate filter ON)
- Count secondary alignments (secondary alignment filter OFF)
Use this VCF for counting:
/home/socci/Code/FillOut/TestMAF_VCF/hotspotList.vcf
/home/socci/Code/FillOut/TestMAF_VCF/hotspotList_8Col.vcfPrograms should work on both and give the same output.
Use these BAMs in:
/ifs/res/share/pwg/NormalCohort/SetA/CuratedBAMsSetA- Proj_WES_Blacklist_v1_indelRealigned_recal_s_A2_N.bam
- Proj_WES_Blacklist_v1_indelRealigned_recal_s_ACC18_N.bam
- Proj_WES_Blacklist_v1_indelRealigned_recal_s_AMB4_N.bam
- Proj_WES_Blacklist_v1_indelRealigned_recal_s_AMB5_N.bam
- Proj_WES_Blacklist_v1_indelRealigned_recal_s_ASCM4_N.bam
- Proj_WES_Blacklist_v1_indelRealigned_recal_s_ASCM6_N.bam
- Proj_WES_Blacklist_v1_indelRealigned_recal_s_ASCM9_N.bam
- Proj_WES_Blacklist_v1_indelRealigned_recal_s_BR1_N.bam
- Proj_WES_Blacklist_v1_indelRealigned_recal_s_DS_bkm_087_N.bam
- Proj_WES_Blacklist_v1_indelRealigned_recal_s_DS_bkm_099_N.bam
The following file has these paths for easy use:
/home/socci/Code/FillOut/TestMAF_VCF/testBAMs_A1.list