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walaj / svaba

Structural variation and indel detection by local assembly
GNU General Public License v3.0
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How can I find contig info of "~~01D"? #117

Closed hadgie closed 2 years ago

hadgie commented 2 years ago

Hello, I am going through the alignments.txt file to search for certain contigs from the sv.vcf file. I can easily find the c_x_xxxxxxxx_xxxxxxx_xxC contigs, but cannot find the contigs that ends with -01D like 1:4204471(-)-1:4204965(+)__1_4189501_4214501D . What could be the main difference of these two identifier type, and is there a way to find the contigs matching the -01Ds?

Thanks in advance.

walaj commented 2 years ago

Hello. The SVs of the type you are looking for are "discordant read-only", meaning that there is no contig to find. They are generally lower quality results, depending on the nature of your sequencing data.

hadgie commented 2 years ago

I see. Thanks for the reply.