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parklab / xTea

Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics
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HERV doesn't generate .vcf and gets error while reading reads_fa folder #82

Closed eduymaz closed 1 year ago

eduymaz commented 1 year ago

Hi!

I cannot generate .vcf results in my HERV file; you have a comment about this https://github.com/parklab/xTea/issues/10#issuecomment-998095493. After the last version, you answered another question about this situation as https://github.com/parklab/xTea/issues/55#issuecomment-1221578041. Do we expect the HERV output still not to produce a .vcf file? If the result file is "candidate_disc_filtered_cns.txt", how can I access the header information of the file?

In addition; I get an error like below during HERV operations. Is this error directly related to the result file? I would appreciate your valuable comment. HERVerror

simoncchu commented 1 year ago

Hi, sorry for the late reply. Yes, still no VCF generated for HERV. It's on my list, but just delayed by other works. I'll try to update soon. The first few columns are chrm, representative-breakpoint, left-breakpoint, right-breakpoint, TSD, left-supporting-clip-reads, right-supporting-clip-reads, left-supporting-discordant-reads, right-supporting-discordant-reads, left-polyA, right-polyA, left-read-depth, right-read-depth...

This error doesn't affect the final results.