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willgdjones/gist:8a3b2ac59a645d4c033a4f0abb22728a

Created April 7, 2016 15:25
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gistfile1.txt
./vg construct -r /lustre/scratch113/projects/graphs/yeast/data/SGD_2010.fasta \
-v /lustre/scratch113/projects/graphs/yeast/data/SGRP2-cerevisiae-freebayes-snps-Q30-GQ30.vcf.gz \
-m 1000 -a > output/yeastgraph.vg\
./vg mod -pl 16 -e 3 output/yeastgraph.vg \
| ./vg mod -S -l 32 - \
| ./vg kmers -gB -k 16 -F -H 1000000000 -T 1000000001 - \
> output/yeastgraph.graph /
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ekg commented Apr 7, 2016

There is a hack here that works. Strip the paths.

vg-81b5a2cb mod -D yeast1.vg | vg-81b5a2cb mod -pl 16 -e 3 - >yeast1.modl16e3.vg

This completes pretty quickly. I'm going to try the last parts of the process and see how it goes.

Something is very wrong with the path manipulation. @adamnovak has reported it I think, but I'm not finding the documentation.

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