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kcleal / dysgu

Toolkit for calling structural variants using short or long reads
MIT License
92 stars 11 forks source link

what is SVLEN？ #63

Closed wenyuhaokikika closed 1 year ago

wenyuhaokikika commented 1 year ago

Thanks to dysgu, it's a really great tool. I have a question during running:

for this image

As shown in the picture above, I think it means that the C at position 1028532 on chromosome 1 is deleted, but the SVLEN is 550 shown in INFO, why? Shouldn't it be 1?

kcleal commented 1 year ago

Hi @wenyuhaokikika,

The start of the SV is at 1028532 on chr1, but the END is listed in the info column as END=1029082. The C indicates that the reference base at the start position is a C. SVLEN is the difference between the start and END. Hope that makes sense.

wenyuhaokikika commented 1 year ago

Thank you so much for your quick reply, I think I get it it means position 1028532-1029082(1028532+550) on chromosome 1 is deleted The main thing that confuses me is that CONTIGA and CONTIGB do not match the genome, so I ignore these two fragments