cn assign to SMN1/2 is confusing

[Soleilcode]

Hi,
Thanks for the convenient tools！I have some confusion for the results. It can be seen that the total copy number of smn in the figure is about 1. The last bar chart shows that smn1 has more copies. Therefore, the distribution should be that the copy number of smn1 is 1 and that of smn2 is 0. I was puzzled by the result.

Aside from this problem, the upon problem is based on the results generated by smncaller. However, this sample is actually a 2+0 silent carrier sample. I use the default parameter of bwa-mem for mapping and then use SMNCopyNumberCaller based on sorted bam file. The result shows that this is a 1+0 sample. What might account for this result? Our data is 30x WGS.

[xiao-chen-xc]

Hi @Soleilcode, does your reference genome include ALT contigs? If so we suggest alt-aware alignment (https://github.com/lh3/bwa/blob/master/README-alt.md) so that alignments to the primary assembly take precedence over ALT contigs.

Also is this Illumina sequencing or a different platform?

[Soleilcode]

thanks for your helping！i remapped with noalt ref, and finally i successfully verified the 2+0 sample!