Bug of vg surject
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8 months ago
Qi • 0

Hello I tried to use vg surject to convert gam to bam, there was a problem here. If i generate the bam from giraffe by parameter '-o bam', the size of bam file is more bigger than bam generated from vg surject. And then, using command 'samtools sort' also cause a loss of file size. Could anyone notice this question? So how can i do?

vg • 577 views
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It might help us to diagnose the problem if you included the exact commands that you used and showed the results that you are concerned about. It would also help if you point out what part of those results is unexpected.

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Thanks your reply! my resulte show below: 5x_pan_sv.bam 1347587601 #converted from gam to bam F1 indel=0.830392 snp=0.932511

5x_pan_all2_test.bam 1403048325 #generated from 'vg giraffe -o bam' directly F1=0.86433 F1=0.93961

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This is still hard to interpret without the commands. What would help is if you literally copied the full UNIX commands along with their results.

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