Variant Caller

This is a Java version of my original Custom Variant Caller written in C++. Java should provide much better readability and more options for multi-threading without compromising the speed too much.

Installation and usage

This application can be compiled with java 17 using the pom.xml maven file, or use the out/artifacts/VariantCaller_jar/VariantCaller.jar archive and then run in the following way:

<input.sam java -jar VariantCaller.jar [options...]
 --reference VAL : Path to the reference file. (default: /reference/hg19.fa)
 --minBaseQ N    : Minimal base quality. (default: 0)
 --minMapQ N     : Minimal mapping quality. (default: 0)
 --threads N     : Maximum number of processing threads (default: 1)
 --tsv VAL       : Path to the output tsv file. (default: stdout)

For example to run this on the sample data run:

<sample_data/example.sam java -jar VariantCaller.jar --reference sample_data/ref.fa

Short functionality description

For more information see the generated java docs in the src/resources folder.

In the core of this utility is a variant caller, which works takes following steps:

• Read given sam file line by line,
• Filter out all reads that:
  • have empty CIGAR string or,
  • have flag 2048 (supplementary alignment) set;
• If two following lines have the same QNAME handle them as pairs, else handle them as reads without a pair,
• Find variants in every pair/read and increment counters for every position,
• If mapQ of a read is lower than filter level, for this read, increment only counters that don't pass quality checks,
• If baseQ for a base in a read is lower than filter level, for this position in this read, increment only counters that don't pass quality checks,
• Print out all found variants

Output abbreviations meanings

• ADFP (Alternate alleles Depth on Forward strand, Pair spans this position): Depth of variant-supporting bases on forward strand (reads2plus), where the pair read spans this position and doesn't report it.
• ADFU (Alternate alleles Depth on Forward strand, pair does Not span this position): Depth of variant-supporting bases on forward strand (reads2plus), where the pair read does not span this position.
• ADRP (Alternate alleles Depth on Reverse strand, Pair spans this position): Depth of variant-supporting bases on reverse strand (reads2minus), where the pair read spans this position and doesn't report it.
• ADRU (Alternate alleles Depth on Reverse strand, pair does Not span this position): Depth of variant-supporting bases on reverse strand (reads2minus), where the pair read does not span this position.
• ADP: Depth of variant-supporting bases on both reads in the pair.
• DP: Total depth