fermikit
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lh3
De novo assembly based variant calling pipeline for Illumina short reads
When I run the command make -f prefix.mak, I get the error fermi.kit/bfc -1s 3g -k 61 -t 16 prefix.ec.fq.gz 2> prefix.flt.fq.gz.log | gzip -1 > prefix.flt.fq.gz /bin/bash: line 1:...
When I try to run the software using: fermi.kit/run-calling -t16 ~/reference.genome/chr19_new.fa prefix.mag.gz | sh, I get the error ERROR: failed to locate the BWA index. Please run 'fermi.kit/bwa index -p...
Without a minimap2 binary under `fermi.kit/` the `-m` option to `run-calling` was failing in a non-obvious way
Hi Heng, I have one sample with PE100 sequence data, and it's multi-lane PE data like "sample.L01.read_1.fq.gz, sample.L01.read_2.fq.gz, sample.L02.read_1.fq.gz sample.L02.read_1.fq.gz". I want to call small variants and structural variations by...
Hi Heng, Thank you for developing the fermikit. I am trying your fermikit tools on a 30x whole genome sequencing population data. I successfully run the fermikit so far. But...
We are working on generating sequence graphs for use as the reference system in vg. I'm completing a first pass at bluntifying the overlap graph that can be pulled out...
Hi Heng, Always interested to test out new software that you put out. I am doing a lot of targeted resequencing with Illumina TruSight Amplicon data of tumour-only samples. I...
Hi, I have 50x simulated 1000g data with ART (http://www.niehs.nih.gov/research/resources/software/biostatistics/art/). I'm trying to run fermikit on this data and our cluster is killing the job when it passes 170G RAM....
Hi Heng, Great tool. Do you have any advice for joint calling of multiple samples? I obtained a reasonable looking call set by first running your `run-calling` script on each...
