CSB5 lofreq issues - Githubissues

CSB5 / lofreq

LoFreq Star: Sensitive variant calling from sequencing data

http://csb5.github.io/lofreq/

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How does LoFreq automatically adapt to changes in coverage?

#148 LiuH2020 opened 17 hours ago
0
Update lofreq2_cluster.py to be compatible with python 3.X

#147 ammaraziz opened 4 days ago
0
lowfreq "not available from current channels"

#146 antonkratz closed 5 days ago
1
Are there any suggested set of hard filters on lofreq indel file

#145 tanu06 opened 3 weeks ago
0
Lofreq viterbi

#144 rahil19 opened 6 months ago
3
Lofreq vcfplot - python version 3 support

#143 saradunaj opened 8 months ago
0
What are the stringent outputs and why do I have different calling results?

#142 ginnyintifa opened 9 months ago
0
MGI T7 or T10 data

#141 Eduardo-Auer closed 3 weeks ago
0
IndexError: list index out of range

#140 min0609 opened 1 year ago
7
subprocess.CalledProcessError: non-zero exit status 1

#139 balayev1 closed 1 year ago
4
HTSLIB Variable

#138 mkadlof opened 1 year ago
2
subprocess.CalledProcessError: non-zero exit status 1

#137 balayev1 opened 1 year ago
0
how to call multiple-sample variants

#136 ChenDepp opened 1 year ago
4
lofreq vcfplot issues

#135 Ge-Wu-pir opened 1 year ago
2
Permant error in the first step

#134 beginner984 opened 1 year ago
1
Problem of forget to indel alignment-quality to your bam-file

#133 Xiang-Leo opened 1 year ago
4
cpus count versus available cpus

#132 EricDeveaud opened 2 years ago
0
Filter depend on number of cores?

#131 bernt-matthias opened 2 years ago
0
Fix: error caused by including the gsl header files.

#130 tcxxxx opened 2 years ago
0
Fixed an error when including gsl header files.

#129 tcxxxx closed 2 years ago
0
lofreq call-parallel will hang forever on subprocess error

#128 tfmorris opened 2 years ago
0
Lofreq call-parallel applies filters with --no-default-filter option specified

#127 gamabunta313 opened 2 years ago
2
Report AF independent of base quality filters

#126 Paprikant opened 2 years ago
1
Warning: Didn't find any variants in input

#125 Ram-Nagar opened 2 years ago
2
lofreq p-value

#124 nelsonerikd opened 2 years ago
0
Variants missing in parallel mode

#123 oleraj opened 2 years ago
2
No sample column

#122 kostasgalexiou opened 2 years ago
0
/bin/sh: line 1: 16782 Killed and CRITICAL [2021-11-30 08:43:03,767]: Following command failed with status 137

#121 gchevignon closed 2 years ago
5
Problem with "lofreq call"

#120 MartinL1106 closed 3 years ago
0
Quality scores

#119 hannahgoldswain opened 3 years ago
1
Force overwrite

#118 robinjugas opened 3 years ago
0
Adding genotype information

#117 charlesfoster opened 3 years ago
7
Using LoFreq-NQ?

#116 fedarko opened 3 years ago
3
Meaning of normal_relaxed, tumor_relaxed, .._stringent (question)

#115 max-vdL opened 3 years ago
0
ERROR in temp file

#114 robertosirica opened 3 years ago
1
I have trouble to run bootstrap

#113 ryao-mdanderson closed 3 years ago
3
Missing Variant with 90% AF

#112 npatel-ah closed 3 years ago
2
lofreq_star-2.1.5_linux-x86-64 : ./lofreq: error while loading shared libraries: libhts.so.3

#111 HagenC closed 3 years ago
3
Issue during the make stage

#110 Lakshay-sethi opened 3 years ago
1
Bcftools pparallel

#109 rdmorin closed 3 years ago
5
merging fails during somatic variant calling (in parallel mode)

#108 rdmorin closed 3 years ago
2
Approximation shortcut

#107 bkille closed 3 years ago
4
Ignore non ACGT positions in reference

#106 andreas-wilm closed 3 years ago
4
Problem finding "htslib_static.mk" on make

#105 dnbuckley closed 3 years ago
3
Warning: indel calls (before filtering) were made without indel alignment-quality

#104 rahil19 opened 4 years ago
7
indelqual 'unknown op 3 for read' error

#103 mattdoug604 opened 4 years ago
9
How to enable lofreq cluster command?

#102 jwsohn closed 4 years ago
1
invalid vcf output (according to Picard)

#101 parlar opened 4 years ago
1
Running lofreq_star-2.1.5_linux-x86-64 on Linux 3.10.0-862.3.3.el7.x86_64 x86_64

#100 HagenC opened 4 years ago
1
AF/SNV quality filters are not appliable together

#99 stefanches7 opened 4 years ago
2