From a BAM file it prepares a list of variant candidates in VCF format, ready for downstream filtering.
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s_3_tair10srt.bam and tair10genome.fas from the directory above as test input.
When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.
- Default parameters only, with the Output.vcf name changed to s_3_tair10.vcf.
This is the same as running this command:
samtools mpileup -Iuf tair10genome.fas s_3_tair10srt.bam | bcftools view -vcg - > s_3_tair10.vcf
For the test case, the output file you will find in the example_data directory is named s_3_tair10.vcf.