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Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.

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Statistics on pindel

Number of watchers on Github 84
Number of open issues 59
Average time to close an issue 3 months
Main language SystemVerilog
Average time to merge a PR 8 days
Open pull requests 12+
Closed pull requests 2+
Last commit over 3 years ago
Repo Created over 7 years ago
Repo Last Updated over 2 years ago
Size 92.1 MB
Organization / Authorgenome
Page Updated
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To compile Pindel you need three things: GNU Make and GCC (which usually are already installed on Linux) and htslib. The last is not installed on Linux by default, but it can be retrieved with:

git clone https://github.com/samtools/htslib

htslib needs to be built before you can start installing Pindel. (Go to htslib's directory, and follow the directions in its 'readme'. At the time of writing this (February 2016) it simply works if you give the commands make and sudo make install.)

To compile Pindel on OS X, you may need to do more work - 'regular' installation under OS X may work, but in some cases OS X gives problems with the OpenMP library Pindel uses for speedup. In those cases, please follow the instruction on the following page to update your gcc


If htslib has been cloned and installed, go to the pindel directory ([my-path]/pindel) and use the INSTALL script there in the following way:

./INSTALL [path-to-htslib]

for example

./INSTALL ../htslib

After this, you can run pindel by using

./pindel [options]

Plain ./pindel without command line options will list all available command line options, the FAQ in the Pindel root directory includes a usage example.

If there are any problems with installing or running Pindel, you may be able to find the solution in the FAQ (the FAQ file stored in the same directory as the INSTALL script), otherwise, feel free to open an issue on github (https://github.com/genome/pindel/issues) or to contact the main author, Kai Ye, at kaiye@xjtu.edu.cn

pindel open issues Ask a question     (View All Issues)
  • almost 4 years pindel2vcf error: the -co setting
  • about 4 years pindel install fail
  • about 4 years pindel2vcf error: unknown argument: –so
  • about 4 years Pindel-C
  • about 4 years Bloated ref counts for variant size <= 2
  • about 4 years Pindel build fails every time on htslib
  • over 4 years make test expected to fail?
  • over 4 years Pindel Output files
  • over 4 years pindel
  • over 4 years Does the depth impact the number of SVs(reverseοΌ‰?
  • over 4 years Insert size with decimal points creates confusion in output
  • over 4 years Two weird problems about Pindel
  • over 4 years bam2pindel / Adaptor uninitialized value error
  • over 4 years unique supporting read counts in pindel >v0.2.5b5
  • over 4 years New Pindel is very aggressive
  • over 4 years Fix for segmentation fault if chromosome name not in reference fasta file
  • over 4 years Infinite loop if file does not exist
  • over 4 years Warn user when other reference genome is used for alignment
  • over 4 years Version 0.2.5b8 OUTPUT interpreting
  • almost 5 years How about different libraries in the same sample
  • almost 5 years Running in parallele (Per Chromosome) yields different Output
  • almost 5 years What is location/position of NT_seq in the Tandem Duplication ?
  • almost 5 years Pindel memory usage
  • almost 5 years How to call somatic Indels with using Pindel
  • almost 5 years Run in parallel chromosome by chromosome
  • about 5 years feature request: support space in filepaths in BAM config file
  • over 5 years not compile with samtools 1.2
  • over 5 years Bug in samtools 0.1.18, request update to newer version
  • almost 6 years translocations only reported between 2 chromosomes
  • almost 6 years segfaults when m_breakDancerMask is accessed outside itself
pindel open pull requests (View All Pulls)
  • Update INSTALL instructions for htslib
  • Linted INSTALL script
  • Use /usr/bin/env to find perl
  • updated the regression test to include pindel2vcf, and removed some d…
  • Use new diff() function for absolute difference between two unsigned coords
  • Fix to allow compilation on Debian 9.0
  • New field to INFO column
  • Support for krand in htslib 1.6
  • Revamping the --somatic_p code in pindel2vcf.cpp
  • Improving the documentation of somatic_filter
  • A fix for unsigned value subtract problem
  • Change InsertSize type from short to int for large sequences
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