- bwa mem alignment
- samtools convert sam to bam
- sambamba sort
- sambamba mark duplication (markdup)
- GATK Haplotype Caller
- GATK GVCFs -> final vcf file
- Annovar -- vcf to annovar input
- Annovar -- table_annovar
http://broadinstitute.github.io/picard/explain-flags.html https://www.samformat.info/sam-format-flag https://www.samformat.info/sam-format-flag-single https://ppotato.wordpress.com/2010/08/25/samtool-bitwise-flag-paired-reads/ https://biobeat.wordpress.com/2013/04/29/directional-rna-seq-part-1-extract-strand-information-from-sam-file/ https://ppotato.files.wordpress.com/2010/08/slide1.png
- Web resource https://www.biostars.org/
After sortd
/pkg/biology/SAMtools/SAMtools_v1.9/bin/samtools index NA12878_MOD_sorted.bam
/pkg/biology/SAMtools/SAMtools_v1.9/bin/samtools flagstat NA12878_MOD_sorted.bam > NA12878_MOD_sorted.bam.flagstat
or
/pkg/biology/SAMtools/SAMtools_v1.9/bin/samtools stats NA12878_MOD_sorted.bam > NA12878_MOD_sorted.bam.stats
Add Or Replace Read Group
https://gatk.broadinstitute.org/hc/en-us/articles/360037226472-AddOrReplaceReadGroups-Picard-