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varcall

By Aronesty E., Last update 1494698998
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varcall description

Varcall takes a pileup and calculates variants in a more easily parameterized manner than some other tools. It does two tasks: (1) calculates error rate statistics in a pileup and (2) outputs variants per position. The tool is not complete. In particular: the VCF output is broken, and the error rate calculations should probably be regional, not global. Also when inputting 'bams' all varcall does is call samtools mpileup. it has no real native bam reader. One of the advantages is the parameterization, allowing varcall to be used in any situation, this is also a shortcoming since users must know the meanings of every parameter.


Parent program: ea-utils

Ea-utils is FASTQ processing utilities such as fastq-mcf, fastq-multx, fastq-join, varcall and sam-stats and other. These tools detect and remove sequencing adapters and primers, detect limited skewing at the ends of reads and clip, poor quality at the ends of reads and clip, discard sequences that are too short after all of the above, keep multiple mate-reads in sync while doing all of the above, merge overlapping paired-end reads and computing statisticsfrom SAM, BAM or Fasta files.