sasha@genomics ~ % whoami
Hi, this is Sasha Chernenkoff
Bioinformatics | Machine Learning | Design
sasha@genomics ~ % bwa mem -t 8 ref.fa sample_R1.fq.gz sample_R2.fq.gz \
| samtools sort -@ 8 -o aligned.bam -
[main] Real time: 512.334 sec; CPU: 3892.011 sec
sasha@genomics ~ % gatk MarkDuplicates -I aligned.bam -O dedup.bam -M metrics.txt
INFO MarkDuplicates - Marking 1,204,338 duplicate reads
sasha@genomics ~ % gatk BaseRecalibrator -I dedup.bam -R ref.fa \
--known-sites dbsnp.vcf.gz -O recal.table
INFO ProgressMeter - Traversal complete. Processed 24,192 regions.
sasha@genomics ~ % gatk ApplyBQSR -I dedup.bam -R ref.fa \
--bqsr-recal-file recal.table -O recal.bam
sasha@genomics ~ % gatk HaplotypeCaller -R ref.fa -I recal.bam \
-O sample.g.vcf.gz -ERC GVCF
INFO HaplotypeCaller - Emitting reference-confidence GVCF records
INFO ProgressMeter - chr1:248,912,033 99.8% 3.2 m
INFO HaplotypeCaller - Total variants called: 4,812,337
sasha@genomics ~ %