NGS workflow 2022-08-03

gunzip *.gz
bwa index Homo_sapiens_assembly38.fasta
bwa mem -t 12  ~/Homo_sapiens_assembly38.fasta Undetermined_S0_L001_R1_001.fastq Undetermined_S0_L001_R2_001.fastq > ~/input/Undetermined_S0_L001.sam
java -jar ~/picard.jar SamFormatConverter -I Undetermined_S0_L001.sam -O Undetermined_S0_L001.bam
samtools faidx Homo_sapiens_assembly38.fasta
java -jar ~/picard.jar CreateSequenceDictionary -R Homo_sapiens_assembly38.fasta -O Homo_sapiens_assembly38.dict
java -jar ~/picard.jar AddOrReplaceReadGroups -I Undetermined_S0_L001.bam -O Undetermined_S0_L001_RG.bam --SORT_ORDER coordinate --RGID foo --RGLB bar --RGPL illumina --RGSM Sample1 --CREATE_INDEX True --RGPU XXX
~/gatk-4.2.6.1/gatk HaplotypeCaller -R ~/Homo_sapiens_assembly38.fasta -I Undetermined_S0_L001_RG.bam -O ~/output/Undetermined_S0_L001.g.vcf.gz