CFSAN-Biostatistics/snp-pipeline

Issues

• Select the subset of the samples

  #28 opened a year ago by ConstantinV
  0

• Picard does't work on java 1.8, GATK 3.8 dose't not work on java 20

  #27 opened 2 years ago by jinyanjane
  4

• CLASSPATH of GATK version 4.4.0.0

  #26 opened 2 years ago by jinyanjane
  4

• Pipeline gets stuck after read mapping.

  #22 opened 2 years ago by dzd5
  5

• how to produce Phylogenetic Tree based on core genome snp

  #16 opened 2 years ago by Galib009
  0

• 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 opened 2 years ago by DagmaraNiedziela
  8

• Pseudo-whole genome alignment from the pipeline?

  #14 opened 2 years ago by cizydorczyk
  1

• Hello!

  #15 opened 2 years ago by Galib009
  0

• running call_sites on indexed bam file

  #7 opened 2 years ago by cb4github
  1

• UnboundLocalError in distance.py:calculate_snp_distances

  #9 opened 2 years ago by crashfrog
  1

• Work Item 1: Refactor from GATK3 to ABRA2

  #24 opened 2 years ago by crashfrog
  0

• Work Item 2: Refactor from PyVCF to PyVCF3

  #25 opened 2 years ago by crashfrog
  0

• classpath configuration error

  #23 opened 2 years ago by saifulislam1997
  0

• BACTERIA ORGANISM WITH TWO CHROMOSOMES

  #20 opened 4 years ago by vappiah
  4

• samtools version check

  #19 opened 4 years ago by rlpires
  4

• Error in SNP filtration step while running with the run option

  #18 opened 4 years ago by parul-sharma
  6

• how to set up input files if I have both Illumina and nanopore long reads for dozens bacterial genomes

  #17 opened 5 years ago by limin321
  1

• New release of picard

  #13 opened 6 years ago by EnzoAndree
  5

• Picard specific error

  #12 opened 7 years ago by mshakya
  6

• CLASSPATH is not configured with the path to Picard

  #11 opened 7 years ago by mshakya
  2

• Doubts about the number of SNPs reported in two output files

  #10 opened 7 years ago by EnzoAndree
  2

• snp_filter.py fail

  #6 opened 8 years ago by gotero
  3

• SAMtools V.1.3.1 error with prep samples

  #5 opened 9 years ago by mstasiewicz
  3

• pipeline halted at mergeVcf.sh

  #4 opened 9 years ago by rodsa
  4

• Error: "$numAlignThreads" contains no decimal number

  #2 opened 9 years ago by fabspagnolo
  3