Commands

The baseqSNV package are relied on several softwares and resources to generate the final results. These informations should be provided to the baseqSNV through a configuration file.

Config File

A config file is needed to for the package to identify the pathes of the softwares and related resources. You can name the file as config.ini.

For human genome version GRCh37(hg19) user, the related configuration files follows:

[SNV]
temp_dir = /tmp
bwa = /mnt/gpfs/Database/softs/anaconda2/bin/bwa
samtools = /mnt/gpfs/Database/softs/anaconda2/bin/samtools
java = /mnt/gpfs/Database/softs/anaconda2/bin/java
GATK = /mnt/gpfs/Users/wufan/p12_HEC/GATK/GATK_code/gatk-4.0.3.0/gatk
picard = /mnt/gpfs/Users/wufan/p12_HEC/GATK/picard.jar

[SNV_ref_hg37]
genome = /mnt/gpfs/Users/wufan/p12_HEC/GATK/resources/ref_b37/hs37d5.fa
bwa_index = /mnt/gpfs/Users/wufan/p12_HEC/GATK/resources/ref_b37/hs37d5.fa
DBSNP = /mnt/gpfs/Users/wufan/p12_HEC/GATK/resources/ref_b37/dbsnp_138.b37.vcf
SNP = /mnt/gpfs/Users/wufan/p12_HEC/GATK/resources/ref_b37/1000G_phase1.snps.high_confidence.b37.vcf
INDEL= /mnt/gpfs/Users/wufan/p12_HEC/GATK/resources/ref_b37/Mills_and_1000G_gold_standard.indels.b37.vcf
omni = /mnt/gpfs/Users/wufan/p12_HEC/GATK/resources/ref_b37/1000G_omni2.5.b37.vcf
hapmap = /mnt/gpfs/Users/wufan/p12_HEC/GATK/resources/ref_b37/hapmap_3.3.b37.vcf
interval = /mnt/gpfs/Users/wufan/p17_wuchen/28wuchen/merge.all.target.1.list
germline = /mnt/gpfs/Users/wufan/p12_HEC/GATK/resources/ref_b37/af-only-gnomad.raw.sites.b37.vcf.gz

[Annovar]
annovar = /mnt/gpfs/Users/wufan/p12_HEC/GATK/annovar_new/annovar
annovar_db_hg38 = /mnt/gpfs/Users/wufan/p12_HEC/GATK/annovar/human38db
annovar_db_hg19 = /mnt/gpfs/Users/wufan/p12_HEC/GATK/annovar_new/annovar/human_hg19

Data File

Description on input samples, tab sepereated values. The first column should be the sample name. The aligned bam or raw sequencing depth are accepted.

ESCCL0051_N501 /mnt/gpfs/Users/wufan/p17_wuchen/d0610/bam/ESCCL0051_N501.final.bam
ESCCL0051_N528 /mnt/gpfs/Users/wufan/p17_wuchen/d0610/bam/ESCCL0051_N528.final.bam
ESCCL0051_N533 /mnt/gpfs/Users/wufan/p17_wuchen/d0610/bam/ESCCL0051_N533.final.bam
ESCCL0051_N579 /mnt/gpfs/Users/wufan/p17_wuchen/d0610/bam/ESCCL0051_N579.final.bam

Commands