deepvariant

#gcr.io/deepvariant-docker/deepvariant
for file in /farmacija.bckup/hg19/chr1.fa
do
echo $file
arrIN=(${file//\// })
echo ${arrIN[2]}
/opt/deepvariant/bin/make_examples --mode calling --ref $file --reads /farmacija.bckup/HKMP-dysl/IonCode_0109_*.bam --examples output.09_${arrIN[2]}.tfrecord
# --regions "chr1:10,000,000-10,010,000"

/opt/deepvariant/bin/call_variants --outfile call_variants_output.09_${arrIN[2]}.tfrecord --examples output.09_${arrIN[2]}.tfrecord --checkpoint ../models/model.ckpt

/opt/deepvariant/bin/postprocess_variants --ref $file --infile call_variants_output.09_${arrIN[2]}.tfrecord --outfile output.09_${arrIN[2]}.vcf

done