Assistance Needed with svtools lsort - No Output Generated

[karen916]

Dear svtools Development Team,

I am currently utilizing svtools version 0.5.1 for processing VCF files generated by LUMPY and have encountered an issue that I have been unable to resolve.

I am attempting to sort and merge VCF files using the svtools lsort command followed by compression with bgzip. The command executes without returning any errors, yet the output file seems to contain no variant data, which is unexpected as the input VCF files do contain variant entries.

Here is the command I used:

svtools lsort ../1-13/lumpy/sample_1-13.vcf.gz ../1-12/lumpy/sample_1-12.vcf.gz | bgzip -c > sorted_test.vcf.gz
After running the command, the resulting sorted_test.vcf.gz file is generated, but when inspecting the file, it appears to be devoid of any variant calls. The original VCF files certainly contain variant data, as confirmed by viewing them directly.

I have checked for potential issues such as file permissions, file encoding, and command syntax, but the problem persists. I have also ensured that my environment has the necessary read/write permissions and that there are no apparent encoding issues with the files.

I would greatly appreciate any guidance or suggestions you might have to troubleshoot this issue. If there are any known compatibility issues with the aforementioned version of svtools or if there are additional logs I could provide, please let me know.

Thank you for your time and assistance. I am looking forward to your valuable input.

Best regards,

Chenzhaojin