.ld file format issue. two additional columns

[jmhallas]

Hello,

I ran ngsLD on a beagle file

ngsLD \
--geno allmdSub.beagle.gz \
--posH allmdSub.pos.gz \
--probs \
--n_ind $NIND \
--n_sites $NSITES \
--max_kb_dist 10 \
--min_maf 0.05 \
--n_threads 16 \
--outH ./allmdSub.ld


==> Input Arguments:
        geno: /share/cdfwwildlife/hallas_dedicated/lc_deer/angsd/allmdSub/allmdSub.beagle.gz
        probs: true
        log_scale: false
        n_ind: 204
        n_sites: 83611
        pos: /share/cdfwwildlife/hallas_dedicated/lc_deer/angsd/allmdSub/allmdSub.pos.gz (WITH header)
        max_kb_dist (kb): 10
        max_snp_dist: 0
        min_maf: 0.050000
        ignore_miss_data: false
        call_geno: false
        N_thresh: 0.000000
        call_thresh: 0.000000
        rnd_sample: 1.000000
        seed: 1681186263
        extend_out: false
        out: /share/cdfwwildlife/hallas_dedicated/lc_deer/ngsld/nallmdSub.ld (WITH header)
        n_threads: 16
        verbose: 1
        version: 1.1.1 (Mar 28 2023 @ 10:46:02)

==> GZIP input file (not BINARY)
> Reading data from file...
> Header found! Skipping line...
==> Calculating MAF for all sites...
==> Getting sites coordinates
==> Launching threads...
==> Waiting for all threads to finish...
==> Freeing memory...
Done!

my output has two additional columns

#site1	site2	dist	r^2_ExpG	D	D'	r^2
HiCscaffold1pilon:548766	390	HiCscaffold1pilon:552772	378	4006	0.008618	0.010649	0.204312	0.026252
HiCscaffold1pilon:544311	396	HiCscaffold1pilon:548766	390	4455	0.024345	0.047307	0.999452	0.318523
HiCscaffold1pilon:552807	356	HiCscaffold1pilon:552811	382	4	0.458927	0.055914	0.999964	0.431553
HiCscaffold1pilon:544239	387	HiCscaffold1pilon:544270	363	31	0.019952	-0.000612	0.033265	0.000030
HiCscaffold1pilon:138487	362	HiCscaffold1pilon:138500	371	13	0.000093	-0.010224	0.433973	0.008593
HiCscaffold1pilon:544311	396	HiCscaffold1pilon:552772	378	8461	0.010669	0.012214	0.163652	0.013607
HiCscaffold1pilon:153019	375	HiCscaffold1pilon:153035	387	16	0.823266	0.244860	0.999997	0.999810

I'm not sure what the second and fourth column represent. Any thoughts?

Thank you for your time,

--josh

[fgvieira]

what is the content of the file allmdSub.pos.gz?

[jmhallas]

chr pos totDepth HiCscaffold1pilon 138487 362 HiCscaffold1pilon 138500 371 HiCscaffold1pilon 150873 329 HiCscaffold1pilon 150942 361 HiCscaffold1pilon 151045 366 HiCscaffold1pilon 151405 384 HiCscaffold1pilon 152517 382 HiCscaffold1pilon 152760 400 HiCscaffold1pilon 153019 375

…

On Wed, May 10, 2023 at 6:28 AM Filipe G. Vieira ***@***.***> wrote: what is the content of the file allmdSub.pos.gz? — Reply to this email directly, view it on GitHub <#45 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AQOUKLXGHHZQREMTHQHXBUTXFOJYVANCNFSM6AAAAAAX35LHJ4> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[fgvieira]

I think 2nd and 4th columns are the 3rd column in your pos file. Can you try removing the third column and run again?

[jmhallas]

Thanks. I'll give it a try. Super weird that my angsd run included the total depth for each position.

…

On Wed, May 10, 2023 at 9:27 AM Filipe G. Vieira ***@***.***> wrote: I think 2nd and 4th columns are the 3rd column in your pos file. Can you try removing the third column and run again? — Reply to this email directly, view it on GitHub <#45 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AQOUKLXNXFFMXLY2IFRZA53XFO6WTANCNFSM6AAAAAAX35LHJ4> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[fgvieira]

Did it work?