select_hetero_snp_for_phasing breaks for contigs where no variants are found

[xingyaoc]

VCFs are not generated for contigs where no variants are found, which breaks select_hetero_snp_for_phasing.
clairs_output/vcf contains these files:

chr1.vcf chr16.vcf chr21.vcf chr22.vcf chr4.vcf chr5.vcf

Errors pasted from some of 1_select_hetero_snp_for_phasing.log:

[INFO] Total HET SNP calls selected: chr22: 119, not found:27, not match:0, low_qual_count:0. Total normal:57 Total tumor:146, pro: 0.815068493150685
Traceback (most recent call last):
File "/opt/bin/clairs.py", line 120, in
main()
File "/opt/bin/clairs.py", line 114, in main
submodule.main()
File "/opt/bin/src/select_hetero_snp_for_phasing.py", line 157, in main
select_hetero_snp_for_phasing(args)
File "/opt/bin/src/select_hetero_snp_for_phasing.py", line 118, in select_hetero_snp_for_phasing
pro = len(pass_variant_dict) / len(tumor_qual_dict)
ZeroDivisionError: division by zero
Traceback (most recent call last):
File "/opt/bin/clairs.py", line 120, in
main()
File "/opt/bin/clairs.py", line 114, in main
submodule.main()
File "/opt/bin/src/select_hetero_snp_for_phasing.py", line 157, in main
select_hetero_snp_for_phasing(args)
File "/opt/bin/src/select_hetero_snp_for_phasing.py", line 118, in select_hetero_snp_for_phasing
pro = len(pass_variant_dict) / len(tumor_qual_dict)
ZeroDivisionError: division by zero
[INFO] Total HET SNP calls selected: chr1: 220, not found:66, not match:0, low_qual_count:0. Total normal:73 Total tumor:286, pro: 0.7692307692307693
[INFO] Total HET SNP calls selected: chr21: 1, not found:1, not match:0, low_qual_count:0. Total normal:31 Total tumor:2, pro: 0.5
Traceback (most recent call last):
File "/opt/bin/clairs.py", line 120, in
main()
File "/opt/bin/clairs.py", line 114, in main
submodule.main()
File "/opt/bin/src/select_hetero_snp_for_phasing.py", line 157, in main
select_hetero_snp_for_phasing(args)
File "/opt/bin/src/select_hetero_snp_for_phasing.py", line 118, in select_hetero_snp_for_phasing
pro = len(pass_variant_dict) / len(tumor_qual_dict)
ZeroDivisionError: division by zero

[zhengzhenxian]

Hi,

Seems no germline variants output found, could you send the ${OUTPUT_DIR}/run_clairs.log to my email address(zxzheng@cs.hku.hk) for us to pinpoint the error?

[xingyaoc]

Hi, Thanks for the response! To give you a bit of context, I am testing ClairS on a random subset of split bams (30/3000 from each tumor and normal, then I merge the bam subset and pass it into ClairS). This is probably why very few variants are being found for both germline and somatic. I have attached the log file as requested. Best, Xingyao

[zhengzhenxian]

Hi, Xingyao,

Thanks for the logs. Some contigs did have no SNPs output owing to the small BAM size. We have fixed the error and please try to re-pull the docker image(You might need to remove your local image first using dcoker rmi hkubal/clairs:latest )

Zhenxian