Hello! I am using vg giraffe to map the short read data(150bp) against HPRC pangenome graph. The mapping rate is about 92% in my test data with a quite low perfectly mapping rate (25%). However, using bwa-mem to map the same data against CHM13 linear reference results in a better mapping rate(98%). To my opinion, mapping to pangenome can reduce the reference bias in mapping. Moreover, the results in MC paper can also prove that giraffe is better than bwa-mem. How can I adjust the parameters to improve the mapping rate? Or how can I prove using giraffe and pangenome reference is better than bwa-mem and linear reference?
•
written
by
gulin •
1 answer
You'll get a lower mapping rate, but a higher number of perfect alignments. That is the improvement. You should get less heterozygous SNPs downstream.
Look here for example at around 38.5 minutes -
Log in to answer this question.
-
Is vg giraffe appropriate for RADseq sequencing reads?
written by RianeZ •
-
VG Crash with HPRC V2.0 Graph and Indexes
written by Alexandria A. •
-
core dumped in vg pack using gaf file
written by gulin •
-
MAPQ algorithms of Giraffe
written by gulin •
-
Question about vg giraffe, vg surject and Visualization tool for mapping result
written by gulin •
-
GRCh38 reference paths in human pangenome
written by Rugare •
-
Unexpected behavior of `vg surject`
written by Ilya •
-
What path list should be used to surject GAM to GRCh38/CHM13 reference genome
written by Hanc •
-
Substantial reduction in read mapping following VG surject
written by peterdfields •
-
vg: Mapping fewer reads to a genome graph than a linear reference
written by John Lloyd •
