Calling SNPs INDELs with SAMtools BCFtools
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Calling SNPs INDELs with SAMtools BCFtools , User should turn on SNP calling, call genotypes at variant sites,and output potential variant sites only options in the bcftools variant calling option panel to get SNPs INDELs calls.employs SAMtools 1.7 mpileup and BCFtools 1.8 call to call SNPs and INDELs
Quick Start
- To use Calling SNPs INDELs with SAMtools BCFtools, import your data in BAM format.
- Resources: http://samtools.sourceforge.net/mpileup.shtml SAMtools 1.7 manual, BCFtools 1.8 manual
Test Data
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Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> Samtools_mpileup. |
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- Use these parameters within the DE app interface:
- Check "SNP calling" in "bcftools view - Consensus/variant calling option" panel
- Check "call genotypes at variant sites" in "bcftools view - Consensus/variant calling option" panel
- Check "output potential variant sites only" in "bcftools view - Consensus/variant calling option" panelSet the mpileup output filename.
- Set the BCFtools call output filename and set the output file type to uncompressed VCF.
- Leave all other parameters as default.
Output File(s)
Expect a bcftools_view_output The output file in the example data generated with these settings is bcftools_1.8_call_output.vcf as output.
Tool Source for App
- http://www.htslib.org/doc/samtools-1.7.html
- https://samtools.sourceforgegithub.netio/bcftools/mpileupbcftools.shtmlhtml