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config.yaml
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config.yaml
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############################################################
# top level directories
sourcedir: /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/callSNPRNA
refanndir: /home/wenjingu/scratch/HPV_fusion/checkMisMatchSample/reference
refdir: /home/wenjingu/remillsscr/HPV_fusion/ref_hg19
############################################################
# reference files, genome indices and data
reference:
stargenomedir:
hg38: $refanndir/SAindex2/
fasta:
hg38: $refanndir/Homo_sapiens_assembly38.fasta
gtf:
hg38: $refdir/gencode.v43.annotation.gtf
1000G:
hg38: $refanndir/1000G_phase1.snps.high_confidence.hg38.vcf.gz
Indels:
hg38: $refanndir/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
star_ref: $refanndir/SAindex
# directory structure for input and output files
datadirs:
fastq: "/home/wenjingu/scratch/HPV_fusion/RNAseq_PE/RNA-data-SNP"
qc: $sourcedir/qc_output
trim: $sourcedir/trimmed_files
bam: $sourcedir/pass1
sj_files: $sourcedir/sj_files
pass2: $sourcedir/pass2
RGbam: $sourcedir/RGbam
dedup: $sourcedir/dedup
splitNcigar: $sourcedir/splitNcigar
Recal1: $sourcedir/Recal1
BQSR_1: $sourcedir/BQSR_1
Recal2: $sourcedir/Recal2
BQSR_2: $sourcedir/BQSR_2
vcf: $sourcedir/vcf
CombinedGvcfs: $sourcedir/CombinedGvcfs
#SNPs filtering Parameters
SNP_SOR: 3.0
SNP_FS: 60.0
SNP_MQ: 40.0
SNP_MQRankSum: -12.5
SNP_ReadPosRankSum: -8.0