The following is an example of utilizing a collection of SNPs selected for our database from the SNPs called in 183 samples.
gatk BaseRecalibrator -I example.bam \
-R reference.fa \
--known-sites glyma.Wm82.gnm2.v0.dbsnp.vcf.gz \
-O recal_data.table
| Tag | File Name | Submitted at | Download |
|---|---|---|---|
| dbSNP | glyma.Wm82.gnm1.v0.dbsnp.vcf.gz | April 12, 2023 |
|
| dbSNP | glyma.Wm82.gnm1.v0.dbsnp.vcf.gz.tbi | April 12, 2023 |
|
| dbSNP | glyma.Wm82.gnm2.v0.dbsnp.vcf.gz | April 12, 2023 |
|
| dbSNP | glyma.Wm82.gnm2.v0.dbsnp.vcf.gz.tbi | April 12, 2023 |
|
| example | example.bam | April 12, 2023 |
|
| example | Glyma1.01.vcf.gz | April 12, 2023 |
|
| dataset | 1309_soybean.vcf.gz | June 5, 2023 |
|