print, extract, convert and call SNPs from BCF
Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> Samtools_mpileup.
Use input.bcf 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.
- Use these parameters within the DE app interface:
- Check "SNP Calling" in "Consensus/variant calling option" panel
- Check "call genotypes at variant sites" in "Consensus/variant calling option" panel
- Check "output potential variant sites only" in "Consensus/variant calling option" panel
Expect bcftools_1.8_view_output as output.