lumpy-sv issues

run lumpy without speedseq

Hi. I want to run lumpy on HPC cluster but do not have speedseq installed. How could I run lumpy with bam files I already have from bwa-mem alignment? Thank...

RafigaM

[E::idx_find_and_load] Could not retrieve index file for '-'

2

hello, I had a problem when i ran lumpyexpress: [E::idx_find_and_load] Could not retrieve index file for '-'. I got this exception, but it generated the vcf file. How should I...

liujiaxin7

ERROR in lumpyexpress -n: command not found; [: ==: unary operator expected

5

Dear LUMPY-SV team, Good evening. When I ran lumpyexpress, I got this message below, Please give me some suggestions or solutions. Thank you so much Clarence --------------------------------------------------------------------------------------- Checking for required...

ClarenceHsiang

Makefile - update BamTools to compile

1

Hi, I'm failing to compile lumpy-sv using the README instructions, specifically the BamTools utils. Would it be possible to update the Makefile for updated instructions to compile BamTools? It seems...

DavidStreid

Input BAM file not found

Hi, I am trying to run lumpyexpress but I am getting the following error despite the bam file exists and the path is correct: > > (base) elpz@picasso:/mnt/scratch/users/b02_cimes_uma/elpz/SVs_manta_normal/021LH19/manta_normal/manta_results> lumpyexpress -B...

espelpz

Error reporting about 'make'

3

/bin/bash: /usr/bin/autoreconf: /usr/bin/perl: bad interpreter: No such file or directory cd lib/htslib && \ ./configure --disable-bz2 --disable-lzma --enable-libcurl /bin/bash: line 1: ./configure: No such file or directory make: *** [htslib]...

zhaobinkai

make compile error

5

When I follow the readme download to make compile, it reports an error, missing file configure.ac: error: required file 'config.sub' not found configure.ac: error: required file 'config.guess' not found configure.ac:...

sjads

Missing pair end parameters:bamfile, histo_file, mean, stdev, read_length, min_non_overlap, discordant_z

Hi lumpy team, I have been working on running lumpy to call large structural variants. I have been running lumpy traditional where I generated insert size distributions following the below...

psardana22