This repository provides comprehensive documentation on the DNA-Seq analysis pipeline adapted from Genomic Data Commons (GDC) for the identification and annotation of somatic variants in whole exome sequencing (WXS) and whole genome sequencing (WGS) data.
For WES, we considered a subsample of FASTQ files from HCC1395. HCC1395 is an epithelial cell isolated from the mammary gland of a 43-year-old, White, female patient with ductal carcinoma TNM Stage I, grade 3. The HCC1395 sample name and sample IDs are as follows: WES_IL_T_1 (SRR7890883).
To subsample the original FASTQ files (code credit goes to one-liner)
# Paste forward and reverse reads side by side, and use awk to format the output
paste SRR7890883_WES_cross-site_study_1.fastq.gz SRR7890883_WES_cross-site_study_2.fastq.gz | \
awk '{ printf("%s",$0); n++;
if(n%4==0) { printf("\n");} else { printf("\t");} }' |
# Use awk to subsample the pairs (adjust k to 50000 for 50,000 reads)
awk -v k=10000 'BEGIN{srand(systime() + PROCINFO["pid"]);}{s=x++<k?x1:int(rand()*x);if(s<k)R[s]=$0}END{for(i in R)print R[i]}' |
# Use awk to split the subsampled pairs into forward and reverse FASTQ files
awk -F"\t" '{print $1"\n"$3"\n"$5"\n"$7 > "WES-IL-T-1-subsampled_1.fastq.gz"; \
print $2"\n"$4"\n"$6"\n"$8 > "WES-IL-T-1-subsampled_2.fastq.gz"}'
For the paired normal, HCC1395 BL (B lymphoblast cell from peripheral blood) should be considered. The sample IDs and sample names are WES_IL_N_1 (SRR7890874).
The tiny FASTQ files are 10K read subsamples of SRR7890883_WES_cross-site_study from benchmark datasets.
# Paste forward and reverse reads side by side, and use awk to format the output
paste SRR7890883_WES_cross-site_study_1.fastq.gz SRR7890883_WES_cross-site_study_2.fastq.gz | \
awk '{ printf("%s",$0); n++;
if(n%4==0) { printf("\n");} else { printf("\t");} }' |
# Use awk to subsample the pairs (adjust k to 50000 for 50,000 reads)
awk -v k=10000 'BEGIN{srand(systime() + PROCINFO["pid"]);}{s=x++<k?x1:int(rand()*x);if(s<k)R[s]=$0}END{for(i in R)print R[i]}' |
# Use awk to split the subsampled pairs into forward and reverse FASTQ files
awk -F"\t" '{print $1"\n"$3"\n"$5"\n"$7 > "SRR7890883_subsampled_1.fastq.gz"; \
print $2"\n"$4"\n"$6"\n"$8 > "SRR7890883_subsampled_2.fastq.gz"}'
The workflow encompasses six main procedures:
Genome Alignment
Alignment Co-Cleaning
Somatic Variant Calling
Variant Annotation
Mutation Aggregation
Aggregated Mutation Masking