-
fastp
-
bwa
-
picard/samtools
-
gatk4 (CNV analysis)
-
mutect2
-
annovar and annovar DB(deprecated)
-
vep and vep DB(very huge ~15G)
-
vcf2maftools
-
MAFtools(only avaliable when multiple sample paired envolved)
-
some in-house script
-
msisensor
-
Dependencies for FREEC
- Control-freeC
- bedtools
- samtools
-
FACET
- snp-pileup
-
NGScheckmate
- bcftools
- python
- samtools
sample input file
TSV file for sample
adjusted from https://github.com/SciLifeLab/Sarek/blob/master/docs/INPUT.md
Input files for ExomeSeqPipe can be specified using a tsv file given to the --sample
parameter. The tsv file is a Tab Separated Value file with columns: subject gender status sample lane fastq1 fastq2
or subject gender status sample bam bai
.
The content of these columns should be quite straight-forward:
subject
designate the subject, it should be the ID of the Patient, or if you don't have one, it could be the Normal ID Sample.gender
is the gender of the Patient, (XX or XY)status
is the status of the Patient, (0 for Normal or 1 for Tumor)sample
designate the Sample, it should be the ID of the Sample (it is possible to have more than one tumor sample for each patient)fastq1
is the path to the first pair of the fastq filefastq2
is the path to the second pair of the fastq filebam
is the bam filebai
is the index
All examples are given for a normal/tumor pair. If no tumors are listed in the TSV file, then the workflow will proceed as if it was a single normal sample instead of a normal/tumor pair.
- Example TSV file for a normal/tumor pair with FASTQ files
In this sample for the normal case there are 3 read groups, and 2 for the tumor. It is recommended to add the absolute path of the paired FASTQ files, but relative path should work also. Note, the delimiter is the tab (\t) character: NOTE: assume each sample has only one libraray
G15511 XX 0 C09DFN pathToFiles/C09DFACXX111207.1_1.fastq.gz pathToFiles/C09DFACXX111207.1_2.fastq.gz
G15511 XX 1 D0ENMT pathToFiles/D0ENMACXX111207.1_1.fastq.gz pathToFiles/D0ENMACXX111207.1_2.fastq.gz
Qi Zhao(zhaoqi@sysucc.org.cn)