I would like to use a VCFtools to evaluate variation data from 48 subjects.
I was given an Excel file that I've since converted to a tab-delimited text file. How should I go about ensuring that the metadata I've added is correct?
Worksheet Variables
- CHROM
- POS
- ID
- REF
- ALT
- QUAL
- FILTER
- INFO (INDEL, IDV, IMF, DP, VDB, SGB, MQSB, MQ0F, ICB, HOB, AC, AN, DP4, MQ, RPB, MQB, BQB, AG)
- FORMAT (GT:PL) (unphased)
- SUBJECT-DATA
Other
- All genotype data is UNPHASED (e.g., 1/2).
- The INFO field was appended to include annotations from SnpEff.
- I understand that the only elements required by VCFtools include "fileformat" and the aforementioned worksheet variables.
For those able to help, please let me know if you would like me to share the metadata I've attempted to piece together (based on the contents of the parent file).
