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(Copied from the lastz mailing list)
we have run lastz version 1.04.15 with --queryhsplimit=keep,nowarn:200 on two softmasked mammalian genomes. The masking comes from repeatMasker. The reason for …
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Hi Andy,
Thanks for developing the cool platypus.
I discover that there is no genotype likelihood for multi-allelic loci and this causes problem when applying beagle to phase the variants.
Do you thin…
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The SVTYPE field in the INFO column is currently described as:
> ## INFO=
>
> Value should be one of DEL, INS, DUP, INV, CNV, BND. This key can be derived from the REF/ALT fields but is useful for …
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Dear,
I used Lumpy via Smoove to call CNVs in a population of ~600 samples.
First, I used 200 high coverage samples to discover CNVs, and then genotyped the sites in the entire population.
In t…
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Hi,
I'm wondering if there's anything I can do with a run of RepeatModeler that is taking a long time with eleredef. Is there a way to skip this step? Or to tell how long it's going to take, or wor…
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I'm getting this error when trying to run vt genotype
```
[parlar@mps 12191-96]$ vt genotype -r /home/bcbio_root/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -s 12191-96 -b 12191-96-ready.bam -o 121…
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I found the DEL size is very long, here are the top ten:
```
1510144027
1475342950
1425352425
1417940033
1388887134
1355193465
1312469728
1297948803
1281732081
1263129094
```
The INV si…
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Hi,
I was wondering if stragler is able to deal with repeat interruption.
For some diseases we can see interruptions of the repeats. Like for Huntington, where the normal repeat CAGCAGCAG... can …
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Starting to noodle on this idea because I think it will be useful for the data structures chapter in R4DS
``` R
# Atomic vectors ----------------------------------------------------------
# Compactl…
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**##This is how my installation looks like:**
manojprasad@mp103:~/3_softwares_installed/mummer-4.0.0beta2$ ls -l
total 88664
-rw-r--r-- 1 manojprasad manojprasad 43542 Oct 14 2017 aclocal.m4
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