ExomePipe

dependencies

• 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

Input file

• sample input file TSV file for sample

adjusted from https://github.com/SciLifeLab/Sarek/blob/master/docs/INPUT.md

TSV file for sample

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 file
• fastq2 is the path to the second pair of the fastq file
• bam is the bam file
• bai 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

Contribution

Qi Zhao(zhaoqi@sysucc.org.cn)