@@ -112,6 +112,8 @@ samtools index -@ $(nproc) -o ${sample}.sorted.deduped.bam.bai ${sample}.sorte | |||
HaplotyperCaller implemented by Google DeepVariant is used to identify germline variants. | |||
#### [DeepVariant](<https://github.com/google/deepvariant>) 1.5.0 | |||
```bash | |||
# Calling variant | |||
deepvariant/bin/run_deepvariant --model_type=WGS --ref=${ref_dir}/${fasta} --reads=${recaled_bam} --output_vcf=${sample}_hc.vcf --num_shards=$(nproc) |