CFSAN-Biostatistics snp-pipeline issues

CFSAN-Biostatistics / snp-pipeline

SNP Pipeline is a pipeline for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organisms sequenced from samples of interest to food safety.

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issues

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Select the subset of the samples

#28 ConstantinV opened 1 year ago
0
Picard does't work on java 1.8, GATK 3.8 dose't not work on java 20

#27 jinyanjane closed 1 year ago
4
CLASSPATH of GATK version 4.4.0.0

#26 jinyanjane opened 1 year ago
4
Work Item 2: Refactor from PyVCF to PyVCF3

#25 crashfrog opened 1 year ago
0
Work Item 1: Refactor from GATK3 to ABRA2

#24 crashfrog opened 1 year ago
0
classpath configuration error

#23 saifulislam1997 closed 2 years ago
0
Pipeline gets stuck after read mapping.

#22 dzd5 closed 1 year ago
5
Error in CFSAN call_consensus: ValueError exception in function __iter__ at line 425 in file /usr/local/lib/python2.7/dist-packages/snppipeline/pileup.py

#21 DagmaraNiedziela closed 1 year ago
8
BACTERIA ORGANISM WITH TWO CHROMOSOMES

#20 vappiah closed 3 years ago
4
samtools version check

#19 rlpires closed 4 years ago
4
Error in SNP filtration step while running with the run option

#18 parul-sharma closed 4 years ago
6
how to set up input files if I have both Illumina and nanopore long reads for dozens bacterial genomes

#17 limin321 closed 4 years ago
1
how to produce Phylogenetic Tree based on core genome snp

#16 Galib009 closed 1 year ago
0
Hello!

#15 Galib009 closed 1 year ago
0
Pseudo-whole genome alignment from the pipeline?

#14 cizydorczyk closed 1 year ago
1
New release of picard

#13 EnzoAndree closed 5 years ago
5
Picard specific error

#12 mshakya closed 6 years ago
6
CLASSPATH is not configured with the path to Picard

#11 mshakya closed 6 years ago
2
Doubts about the number of SNPs reported in two output files

#10 EnzoAndree closed 6 years ago
2
UnboundLocalError in distance.py:calculate_snp_distances

#9 crashfrog closed 1 year ago
1
Updates to Dockerfile

#8 crashfrog closed 5 years ago
0
running call_sites on indexed bam file

#7 cb4github closed 1 year ago
1
snp_filter.py fail

#6 gotero closed 7 years ago
3
SAMtools V.1.3.1 error with prep samples

#5 mstasiewicz closed 8 years ago
3
pipeline halted at mergeVcf.sh

#4 rodsa closed 8 years ago
4
Checking for key executables

#3 lskatz opened 8 years ago
0
Error: "$numAlignThreads" contains no decimal number

#2 fabspagnolo closed 9 years ago
3
Dockerfile for automated docker builds

#1 crashfrog closed 9 years ago
0