Hello, I am new to the field of NGS data analysis and currently analyzing WES data from tumor samples with matched ones (paired-end, illumina). I am using linux command to analyze the data. This is what I did till now for each sample:
fastqc sample.fastq java -jar trimmomatic-0.38.jar PE sample_1.fastq sample_2.fastq -basedout sample LEADING:30 TRAILING:30 MINLEN:50 bowtie2-build hg38.fa hg38 bowtie2 -x hg38 -1 sample_1P -2 sample_2P -S sample.sam samtools view -bS sample.sam > sample.bam samtools sort sample.bam -o sample.sorted.bam samtools mpileup -uf hg38.fa sample.sorted.bam > sample.mpileup
I don’t know after this step what is the reasonable step to take? I am keen on finding somatic and germline variations. I am using varscan, however I am confused. Shall I use
“ java -jar VarScan.jar somatic normal.pileup tumor.pileup “?
what is different between pileup and mpileup file?
Any help will be very appreciated. Thanks