smooth maf output file question about pggb HOT 8 CLOSED

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Thank you! I was trying to use MAF output to confirm that the graph generated is depicting real insertions/deletions, I wanted to extract sequences for a sample from a particular genomic region where we know there is an insertion/deletion for that sample. For example, there is a big deletion at chromosome 2: 100456-101675 for sample1 which is one of the samples in graph genome. How can I relate this information to the graph to confirm there actually is a deletion in that region? Thank you!

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Thank you @ekg! I noticed that pggb graph arranges the sample in alphabetical order. I tried to rearrange the sample order in the step while making chromosome wise files. But the pggb graph again was in alphabetical order. Is there any option to rearrange the sample order?

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I am currently running another job for the same and will update how it goes.

I want to ask that I used deconstruct as per your suggestion:
vg deconstruct sample.xg -g sample.gbwt > sample_deconstruct.vcf

I made sample.gbwt as:
vg gbwt -G graph.fixed.gfa -p -o sample.gbwt

and sample.xg as:
vg convert -x -g graph.fixed.gfa > sample.xg
I am trying to understand the output vcf format. How can I get rid of Consensus as the sample names in the vcf header. I only want to keep the sample names that I used in graph construction.

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If you want to remove the Consensus sample names, you have to remove these from the final smoothed GFA. We do this now by default, when we call vg deconstruct. Please see

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@userzxyz Were you able to solve your problem?

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