<GATK>_<dataset_id>_<sample_id>.g.vcf.gz |
Per-sample GVCF |
<GATK>_<dataset_id>_<sample_id>.g.vcf.gz.sha512 |
Per-sample GVCF checksum |
<GATK>_<dataset_id>_<sample_id>.g.vcf.gz.tbi |
Per-sample GVCF index |
<GATK>_<dataset_id>_<sample_id>.g.vcf.gz.tbi.sha512 |
Per-sample GVCF index checksum |
<GATK>_<dataset_id>_<patient_id>.vcf |
Raw variant calls |
<GATK>_<dataset_id>_<patient_id>.vcf.idx |
Raw variant calls index |
<GATK>_<dataset_id>_<patient_id>_VQSR-SNP-AND_INDEL.vcf.gz |
SNP and INDEL recalibrated variants |
<GATK>_<dataset_id>_<patient_id>_VQSR-SNP-AND_INDEL.vcf.gz.sha512 |
SNP and INDEL recalibrated variants checksum |
<GATK>_<dataset_id>_<patient_id>_VQSR-SNP-AND_INDEL.vcf.gz.tbi |
SNP and INDEL recalibrated variants index |
<GATK>_<dataset_id>_<patient_id>_VQSR-SNP-AND_INDEL.vcf.gz.tbi.sha512 |
SNP and INDEL recalibrated variants index checksum |
<GATK>_<dataset_id>_<patient_id>_snv.vcf.gz |
Filtered SNVs with non-germline and ambiguous variants removed |
<GATK>_<dataset_id>_<patient_id>_snv.vcf.gz.tbi |
Filtered germline SNVs index |
<GATK>_<dataset_id>_<patient_id>_snv.vcf.gz.sha512 |
Filtered germline SNVs sha512 checksum |
<GATK>_<dataset_id>_<patient_id>_indel.vcf.gz |
Filtered INDELs with non-germline and ambiguous variants removed |
<GATK>_<dataset_id>_<patient_id>_indel.vcf.gz.tbi |
Filtered germline INDELs index |
<GATK>_<dataset_id>_<patient_id>_indel.vcf.gz.sha512 |
Filtered germline INDELs sha512 checksum |
report.html, timeline.html and trace.txt |
Nextflow report, timeline and trace files |
*.command.* |
Process specific logging files created by nextflow |