zhou-lab/biscuit

Issues

• Another SNP calling error

  #9 opened 8 years ago by jdidion
  3

• [fetch_refseq:40] Error, cannot retrieve reference chr1:0-0.

  #3 opened 9 years ago by ttriche
  16

• paired end reads overlap

  #48 opened 3 years ago by hmyh1202
  1

• [Issue] pileup "feature"

  #47 opened 3 years ago by vpbrendel
  4

• [Issue] wrong tsv output produced by pileup.c

  #46 opened 3 years ago by vpbrendel
  0

• Conversion Rate calculation

  #45 opened 3 years ago by Irfanwustl
  2

• Weird rectangle output

  #44 opened 4 years ago by weishwu
  0

• CpG Methylation Calculation from bam file

  #43 opened 4 years ago by Irfanwustl
  0

• one read has different CIGAR and read length

  #42 opened 4 years ago by alexyfyf
  0

• Compilation problem: Fail to create biscuit binary

  #41 opened 5 years ago by PanZiwei
  0

• How is downstream analysis impacted for non-directional bisulfite-sequencing libraries aligned in non-directional mode with biscuit?

  #40 opened 5 years ago by meb326
  0

• Is biscuit used for methylation calling only?

  #39 opened 5 years ago by AndyWangSFU
  0

• Position of all cytosines in retention pattern

  #37 opened 5 years ago by shahmj
  0

• make vcf2bed work with multiprocess

  #36 opened 5 years ago by efratushava
  0

• Get biscuit version into a file

  #34 opened 5 years ago by efratushava
  2

• Install biscuit with conda

  #33 opened 5 years ago by efratushava
  0

• lib/aln/bntseq.c:36:10: fatal error: encode.h: 没有那个文件或目录

  #32 opened 5 years ago by ryomawave
  1

• Precompiled download error

  #31 opened 5 years ago by Irfanwustl
  1

• How to prepare for setup_file and files in setup_file?

  #30 opened 6 years ago by xflicsu
  1

• Does the -p option allow an interleaved fastq file as input to biscuit align?

  #21 opened 8 years ago by dhspence
  1

• Collapse strands at CpGs in vcf2bed

  #29 opened 6 years ago by chrisamiller
  3

• alignment and markdup queries

  #27 opened 6 years ago by PoisonAlien
  4

• Make biscuit markdup readgroup-aware

  #28 opened 6 years ago by okartal
  0

• Dose biscuit can used to calculate the ratio of HCG and GCH in each genome site for human? Can I use "biscuit vcf2bed -k 10 -t hcg/gch"? And what's the meaning of colnom 4?

  #25 opened 6 years ago by liuzhe93
  7

• Header for snp bed file

  #26 opened 6 years ago by smcnew
  2

• vcf2bed segmentation fault

  #22 opened 6 years ago by ZhenyuZ
  6

• pileup question/bug?

  #24 opened 6 years ago by ml4wc
  0

• Typo in VCF header causing issues with pyVCF parsing

  #23 opened 7 years ago by aays
  1

• How can I cite biscuit as a reference in my paper?

  #19 opened 8 years ago by lijinbella
  6

• bam generated with bwa-meth

  #17 opened 8 years ago by PoisonAlien
  3

• meaning of vcf2bed output

  #20 opened 8 years ago by vanhzh
  2

• biscuit pileup GT format output as Integer

  #18 opened 8 years ago by GreenInnovator
  1

• SNP calling and known genotypes (question + feature suggestion)

  #16 opened 8 years ago by jdidion
  2

• limit number samples biscuit

  #15 opened 8 years ago by jleluyer
  0

• biscuit asm fails on generated epiread files

  #13 opened 8 years ago by ttriche
  3

• biscuit markdups

  #6 opened 8 years ago by will-NYGC
  4

• Add vcf2bed option to specify sample column

  #12 opened 8 years ago by jdidion
  0

• segfaults & floating point exceptions with -p and/or -c

  #11 opened 8 years ago by ttriche
  1

• C&T Counts from biscuit vcf2bed?

  #10 opened 8 years ago by timpeters82
  2

• Segmentation fault when SNP calling

  #8 opened 8 years ago by jdidion
  10

• Add parameters to ignore biased read positions

  #7 opened 8 years ago by jdidion
  0