Explain the inputs. commads and outputs

[rhondene]

Hi,
when run NASTRA on my bam file (amplicon library), it seems your samtools call is filtering for hg38 regions that are not present in my bam.
What is the proper way general way to run this tool ?
What does the inputs look like?
Example:

python  nastra.py call -b ../c52_fals_data/fALS_diseased.bam -o ../test_NASTRA/ --samtools  path/bin/samtools

>main_samview] region "chr12:12449924-12450059" specifies an invalid region or unknown reference. Continue anyway.

[renzilin]

Hi @rhondene ,

if you want to apply the NASTRA on specific locus, please refer to files in this link.

In detail, we provide the panel file, which provide the hg19 postion of the locus. And the repeat pattern for repeat unit information, while the threshold can be used for genotyping. You can open these files directly.

You can modify these files directly if you want to genotype a new locus.

Best,
Zilin