Closed nick-youngblut closed 3 years ago
+1
Hi @nick-youngblut, apology for the late reply. While we work on the improving the documentation of gt-pro, I would like to explain the 8 output columns of the gtp-paser.py
:
104644 2362409 NODE_941_length_29304_cov_26.5595 22202 G A 20 0
104644 2362412 NODE_941_length_29304_cov_26.5595 22205 C T 20 0
104644 2383325 NODE_990_length_27497_cov_21.326 13814 G T 0 1
104644 2394405 NODE_990_length_27497_cov_21.326 24894 C T 1 0
col 1: the unique 6-digit species id
col 2: 0-based global genomic position across contigs
col 3: contig_id
for the representative genome in the gt-pro k-mer database
col 4: 0-based genomic position within current contig_id
col 5: gt-pro db major allele for current genomic position from current contig (note this is not necessarily the REF allele)
col 6: gt-pro db minor allele
col 7: read counts carrying major alleles
col 8: read counts carrying minor alleles
Please let me know if you have more questions. Thank you..
Chunyu
I was just looking through the docs and couldn't find a description of the output columns. I almost forgot that the description was in this issue. It could be helpful to include this info in the README or tutorial
Sorry for the late reply. Yes, we agree! We now added the description of such in the main docs.
There's no header generated for the
gtp_parse.py
output table, and I don't see a description of the output table columns in the README or wiki. What are the columns? It would be helpful to include a description of the columns in thegtp_parse.py
help docs and/or the gt-pro repo docs.