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Hi all,
Recently I used populations with parameters -s -V to calculate Fst. And now I am stuck by 2 problems:
I got a VCF file but I can't find an index for it. I still can't build index by myself because this is a de novo SNP calling. How can I view this VCF file on IGV without a reference?
I got a new batch_1.maker.tsv file, but I didn't see any sql file. How can I import these data to mql database?
This is my first time to use Stacks, can anyone help me figure out these problems?
Thanks!
my workflow is:
I cut rad tags because of their poor quality (a bunch of N included ) and pooled the reads according to barcodes by myself. I used denovo_map.pl to call SNPs and build mql database. All these steps worked well. Then I use populations to calculate Fst.
Recently I used populations with parameters -s -V to calculate Fst. And now I am stuck by 2 problems:
I got a VCF file but I can't find an index for it. I still can't build index by myself because this is a de novo SNP calling. How can I view this VCF file on IGV without a reference?
I got a new batch_1.maker.tsv file, but I didn't see any sql file. How can I import these data to mql database?
This is my first time to use Stacks, can anyone help me figure out these problems?
Thanks!
my workflow is:
I cut rad tags because of their poor quality (a bunch of N included ) and pooled the reads according to barcodes by myself. I used denovo_map.pl to call SNPs and build mql database. All these steps worked well. Then I use populations to calculate Fst.
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