inumanag
commented
10 months ago Duplicate of #59 ; will publish the fix soon! Thanks for the report!
Closed chrisEisenhartBitscopic closed 10 months ago
inumanag
commented
10 months ago Duplicate of #59 ; will publish the fix soon! Thanks for the report!
Hello, hope all is well. I haven noticed that the -n and --cn-neutral-region commands do not update my neutral region. Is there a way I can provide an updated neutral region to the algorithm?
Example commands;
[ceisenhart@localhost foo]$ aldy genotype --cn-neutral-region chr1:10000-20000 -p illumina -g final.bam 🐿 Aldy v4.4 (Python 3.9.16 on Linux 5.14.0-284.25.1.el9_2.x86_64-x86_64-with-glibc2.34) (c) 2016-2023 Aldy Authors. All rights reserved. Free for non-commercial/academic use only. Genotyping sample POC_LAB_1_S19_L00N_R1_001.true.final.bam... ERROR: gene= cyp2d6, profile= illumina, file= POC_LAB_1_S19_L00N_R1_001.true.final.bam CN-neutral region 22:42151472-42152258 has no reads. Double check your input file for CYP2D8 (are you using hg19?), or pass an alternative CN-neutral region via -n parameter.
[ceisenhart@localhost foo]$ aldy genotype -n chr1:10000-20000 -p illumina -g final.bam 🐿 Aldy v4.4 (Python 3.9.16 on Linux 5.14.0-284.25.1.el9_2.x86_64-x86_64-with-glibc2.34) (c) 2016-2023 Aldy Authors. All rights reserved. Free for non-commercial/academic use only. Genotyping sample POC_LAB_1_S19_L00N_R1_001.true.final.bam... ERROR: gene= cyp2d6, profile= illumina, file= POC_LAB_1_S19_L00N_R1_001.true.final.bam CN-neutral region 22:42151472-42152258 has no reads. Double check your input file for CYP2D8 (are you using hg19?), or pass an alternative CN-neutral region via -n parameter.
I provide an updated copy number region (chr1:10000-20000) and the algorithm still looks for the internally defined region (22:42151472-42152258) then fails when it is not found.
PS: I've noticed similar behavior when trying to specify hg38 as the genome using --genome hg38. The algorithm still runs with hg19 as if I did not specify.