for i in S1A ; do
>
> echo "RUN CMD: gatk --java-options '-Xmx20g' HaplotypeCaller -R $REF \
> -I $workdir/3.map/result/${i}.sorted.dedup.bam \
> -O ${i}.g.vcf.gz --max-alternate-alleles 4 --sample-ploidy 2 \
> -ERC GVCF --tmp-dir $tmpdir"
>
> gatk --java-options "-Xmx20g" HaplotypeCaller -R $REF \
> -I $workdir/3.map/result/${i}.sorted.dedup.bam \
> -O ${i}.g.vcf.gz --max-alternate-alleles 4 --sample-ploidy 2 \
> -ERC GVCF --tmp-dir $tmpdir
> done
