HELLO.
I am currently working on detecting archaic introgression into Sardinian population as a thesis project. And i was trying to use hmmix for this task .
So, as indicated in the documentation i skipped the Find derived variants in outgroup and Estimate local mutation rate steps , and started directly with Finding variants which are not derived in the outgroup.
In this case, i have a question about the -outgroup= of the hmmix create_ingroup . Which outgroup file exactly should i use , i tried with the Outgroup_1000g_HGDP_hg19.txt file provided along with the other useful files, but the obs.txt outputs i obtained were all empty.
I hope i can get a clarification and Thank you in advance.
HELLO. I am currently working on detecting archaic introgression into Sardinian population as a thesis project. And i was trying to use hmmix for this task . So, as indicated in the documentation i skipped the Find derived variants in outgroup and Estimate local mutation rate steps , and started directly with Finding variants which are not derived in the outgroup. In this case, i have a question about the -outgroup= of the hmmix create_ingroup . Which outgroup file exactly should i use , i tried with the Outgroup_1000g_HGDP_hg19.txt file provided along with the other useful files, but the obs.txt outputs i obtained were all empty. I hope i can get a clarification and Thank you in advance.