扩增子测序数据分析 fq.gz --- >vcf

fq1=2
fq1_clean=4
sample=$5
adapter1='AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'
adapter2='AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT'

ref = hg19.fa

mkdir sample
/soft/Bioinformatics/softwares/bioinformatics/hzhang/miniconda3/bin/fastp
-i fq2
-o fq2_clean
--adapter_sequence adapter2
--average_qual 20
--n_base_limit 5
--length_required 50
-w 16

/soft/Bioinformatics/softwares/bwa-0.7.15/bin/bwa mem
-t 16 -k 32 -M -R "@RG\tID:ZFC5818\tLB:ZFC5818\tSM:ZFC5818\tPL:ILLUMINA"
/resource/GV/ref_genome/hg19/bwa-0.7.15/human_hg19.fa
fq2_clean
|samtools view -Su -
|samtools sort
-o ${sample}.bwa.srt.bam -

samtools flagstat -@ 10 {sample}.bwa.srt.bam.stat
samtools stats -@ 10 {sample}.bwa.srt.bam.stat2

echo data
samtools index -@ 16
${sample}.bwa.srt.bam

sambamba depth base -c 0 -t 4
-L /home/works/tmp/panel.bed
{sample}.raw.depth

call_vcf -t {sample}.bwa.srt.bam -o $sample -b cancer_ampliseq_panel.bed -c vardict -v hg19 --thread 30

fastq

fq=fq
>${fq}.fastqc

sambamba depth

/soft/Bioinformatics/softwares/bioinformatics/hzhang/miniconda3/bin/sambamba depth base -c 0 -t 4
-L bed
sample.bwa.srt.bam
> sample.raw.depth