Zev Kronenberg

config error

3

jellyfish]$ autoreconf -i gtest.mk:5: error: Libtool library used but 'LIBTOOL' is undefined gtest.mk:5: The usual way to define 'LIBTOOL' is to add 'LT_INIT' gtest.mk:5: to 'configure.ac' and run 'aclocal' and...

Is it possible to extract kmers in bubbles?

5

Greetings, I was wondering is it possible to extract kmers that are in bubbles? I see the `bubbles` command generates only the variable bases, not fixed width kmers. In otherwords,...

Cleanup PL, GL after filter or primitive

6

@chapmanb @NeillGibson @ekg I've opened this as issue: https://github.com/chapmanb/bcbio-nextgen/issues/1334#issuecomment-209889848 The cleanup will need to be implemented in each tool as there is no way to know which PLs to remove...

Documentation for trio eval

3

Dear Heng, Trying out the trio eval tool, it's a great addition. Can you share the meaning of S/W/H records? I'm guessing an `S` is a sequence? S ctg.000223F 13...

It'd be nice if you could index on custom columns.

can a summation over all counts be added?

feature requests for output VCF

1

Hello, A few requests regarding the output VCF. 1. It would be really useful if the REF/ALT alleles could be populated via the graph traversal. Most users won't know how...

Invalid read names error

4

I'm trying to run iris on long-read SV calls (read alignment based calling: sniffles/pbsv). When running iris via jasmine I get an error about the read name field being invalid....

Jasmine produces invalid VCF

1

bcftools sort exits with the error below. I tested the same sort on all the input files eliminating the possibility that the inputs are problematic. 1. Jasmine is not constructing...

Question: Does Squid work on ISO-seq?

1

We have ISO-seq alignments using gmap2, Will squid run on these data?