`--name` parameter does not work

[bounlu]

Here are my variables:

threads=32
mount_dir="/data/omeran"
out_dir="sv_calling"

normal_bam="LC_AC_normal.bam"
tumor_bam="LC_AC_tumor.bam"

Here is my command line:

smoove call -x \
    --name LC_AC \
    --exclude $mount_dir/$out_dir/ref/exclude.cnvnator_100bp.GRCh38.20170403.bed \
    --fasta $mount_dir/genome.fa \
    --outdir $mount_dir/$out_dir/smoove \
    --genotype \
    --duphold \
    $mount_dir/$out_dir/biscuit/$normal_bam \
    $mount_dir/$out_dir/biscuit/$tumor_bam

Here is the output:

$ ls -a smoove/
-rw-r--r-- 1 omeran omeran  32M Aug 17 21:42 .disc.bam.tmp.bam
-rw-r--r-- 1 omeran omeran 6.0K Aug 17 21:40 .histo
-rw-r--r-- 1 omeran omeran  22M Aug 17 21:42 .split.bam.tmp.bam

[brentp]

you'll need to have read groups with SM in your bams in order to use smoove. The --name only applies to the output, but smoove uses the readgroup sample name internally

[bounlu]

hmm, I do have read group but only with ID field. I will need to add SM then. it would be nice to have this documented somewhere. thanks.

[bounlu]

adding SM to @RG made it work. thanks again.