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SNPsplit - allele-specific alignment sorting

Function A tool to determine allele-specific alignments from high-throughput sequencing experiments that have been aligned to N-masked genomes
Language Perl
Requirements A functional version of Samtools is required.
Code Maturity Stable. SNPsplit has been successfully used for different applications and genomes.
Code Released Yes, under GNU GPL v3 or later.
Initial Contact Felix Krueger

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SNPsplit is an allele-specific alignment sorter which is designed to read in alignment files in SAM/BAM format and determine the allelic origin of reads that cover known SNP positions. For this to work a library must have been aligned to a genome which had all SNP positions masked by the ambiguity base 'N', and aligned using aligners that are capable of using a reference genome which contains ambiguous nucleobases, such as Bowtie 2 or TopHat. In addition, a list of all known SNP positions between the two different genomes must be provided using the option --snp_file.

It is probably worth mentioning that the determination of overlaps correctly handles the CIGAR operations M (match), D (deletion in the read), I (insertion in the read) and N (skipped regions, used for splice mapping by TopHat). Other CIGAR operations are currently not supported.

SNPsplit is now also available on Github where you can find the latest development version SNPsplit (Github)

Here you can access the documentation for more information on the SNPsplit workflow SNPsplit User Guide (pdf).

Here is an example paired-end SNPsplit report SNPsplit PE report (pdf)

Here is an example SNPsplit report for a BS-Seq experiment SNPsplit BS-Seq report (pdf)

Here is an example SNPsplit report for a Hi-C experiment SNPsplit Hi-C report (pdf)