Ecosyste.ms: Issues

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GitHub / CFSAN-Biostatistics/snp-pipeline issues and pull requests

#28 - Select the subset of the samples

Issue - State: open - Opened by ConstantinV about 1 year ago

#27 - Picard does't work on java 1.8, GATK 3.8 dose't not work on java 20

Issue - State: closed - Opened by jinyanjane over 1 year ago - 4 comments

#26 - CLASSPATH of GATK version 4.4.0.0

Issue - State: open - Opened by jinyanjane over 1 year ago - 4 comments

#25 - Work Item 2: Refactor from PyVCF to PyVCF3

Issue - State: open - Opened by crashfrog over 1 year ago

#24 - Work Item 1: Refactor from GATK3 to ABRA2

Issue - State: open - Opened by crashfrog over 1 year ago

#23 - classpath configuration error

Issue - State: closed - Opened by saifulislam1997 about 2 years ago

#22 - Pipeline gets stuck after read mapping.

Issue - State: closed - Opened by dzd5 about 3 years ago - 5 comments

#20 - BACTERIA ORGANISM WITH TWO CHROMOSOMES

Issue - State: closed - Opened by vappiah over 3 years ago - 4 comments

#19 - samtools version check

Issue - State: closed - Opened by rlpires over 4 years ago - 4 comments

#18 - Error in SNP filtration step while running with the run option

Issue - State: closed - Opened by parul-sharma over 4 years ago - 6 comments

#16 - how to produce Phylogenetic Tree based on core genome snp

Issue - State: closed - Opened by Galib009 over 4 years ago

#15 - Hello!

Issue - State: closed - Opened by Galib009 over 4 years ago

#14 - Pseudo-whole genome alignment from the pipeline?

Issue - State: closed - Opened by cizydorczyk almost 5 years ago - 1 comment

#13 - New release of picard

Issue - State: closed - Opened by EnzoAndree over 6 years ago - 5 comments

#12 - Picard specific error

Issue - State: closed - Opened by mshakya over 6 years ago - 6 comments

#11 - CLASSPATH is not configured with the path to Picard

Issue - State: closed - Opened by mshakya over 6 years ago - 2 comments

#10 - Doubts about the number of SNPs reported in two output files

Issue - State: closed - Opened by EnzoAndree almost 7 years ago - 2 comments

#9 - UnboundLocalError in distance.py:calculate_snp_distances

Issue - State: closed - Opened by crashfrog almost 7 years ago - 1 comment
Labels: bug

#8 - Updates to Dockerfile

Pull Request - State: closed - Opened by crashfrog almost 7 years ago

#7 - running call_sites on indexed bam file

Issue - State: closed - Opened by cb4github about 7 years ago - 1 comment

#6 - snp_filter.py fail

Issue - State: closed - Opened by gotero almost 8 years ago - 3 comments

#5 - SAMtools V.1.3.1 error with prep samples

Issue - State: closed - Opened by mstasiewicz over 8 years ago - 3 comments

#4 - pipeline halted at mergeVcf.sh

Issue - State: closed - Opened by rodsa over 8 years ago - 4 comments

#3 - Checking for key executables

Pull Request - State: open - Opened by lskatz almost 9 years ago

#2 - Error: "$numAlignThreads" contains no decimal number

Issue - State: closed - Opened by fabspagnolo over 9 years ago - 3 comments

#1 - Dockerfile for automated docker builds

Pull Request - State: closed - Opened by crashfrog over 10 years ago