Hey so i am encountering an issue while generating the beagle file.
The problem is that my BAM files still have X/Y/MT in their headers because they were originally aligned to the full reference. I thought of using -rf to tell ANGSD to analyse only the 359 NW contigs (currently using ANGSD0.935). But when I used -rf i saw that some sites were duplicated in the BEAGLE file. For example, NW_026622763.1_1000 appeared twice and if you see the below line it is looking for 1077 regions which is 3 times of 359, every row is getting duplicated exactly the same.
Allocated ~ 70 million nodes to the nodepool, this is not an estimate of the memory usage
-> Printing at chr: NW_026622763.1 pos:109647237 chunknumber 160700 contains 557 sitess -> Region lookup 2/1077
Also in my mafs.gz file
zgrep -w "1000" nw_only_v2.mafs.gz | head
the output i got is this
gzip: nw_only_v2.mafs.gz: unexpected end of file
2
NW_026622763.1 1000 C A C 0.000002 6
3
NW_026622763.1 1000 C A C 0.000002 6
So i did a testrun now by using just one region of my -r NW_026622763.1
and i got this -> Region lookup 1/1
that means there is some issue with -rf, this is what i think. What should i do?
Hey so i am encountering an issue while generating the beagle file.
The problem is that my BAM files still have X/Y/MT in their headers because they were originally aligned to the full reference. I thought of using -rf to tell ANGSD to analyse only the 359 NW contigs (currently using ANGSD0.935). But when I used -rf i saw that some sites were duplicated in the BEAGLE file. For example, NW_026622763.1_1000 appeared twice and if you see the below line it is looking for 1077 regions which is 3 times of 359, every row is getting duplicated exactly the same.
Also in my mafs.gz file
zgrep -w "1000" nw_only_v2.mafs.gz | head
the output i got is this
gzip: nw_only_v2.mafs.gz: unexpected end of file
2
NW_026622763.1 1000 C A C 0.000002 6
3
NW_026622763.1 1000 C A C 0.000002 6
So i did a testrun now by using just one region of my -r NW_026622763.1
and i got this -> Region lookup 1/1
that means there is some issue with -rf, this is what i think. What should i do?