What's the format of the bed file for plotting?

[mocksu]

The manual has the following command to plot

IND='HG02481'; python plot_karyogram.py
--bed_a ${IND}_A.bed
--bed_b ${IND}_B.bed
--ind ${IND}
--out ${IND}.png

What's the format of the .bed file? Can you give an example? Does it look like the following?

21 100 200 EUR
21 200 800 AFR
...

One .bed file for hap1, and the other for hap2?

Thanks so much!

[cwarden45]

I think this is what you are looking for: slowkoni/rfmix#15 (comment)

Yes, the input is two .bed files, but it looks different than you provided (and it doesn't strictly confirm to the .bed file format). I've copied over the relevant part of that issue thread here:

I figured out the "TRACTS-compatible" .bed format here:

https://github.com/sgravel/tracts

Also, I had to set "X" to "23" in the centromeres_hg19.bed file, in order to get a .bed file in the following format to work:

1	1	249250621	ACB	0	293.397000284835
2	1	243199373	ACB	0	274.878930310443
3	1	198022430	ACB	0	227.853358434947
4	1	191154276	ACB	0	220.303824741903
5	1	180915260	ACB	0	208.956219767350
6	1	171115067	ACB	0	198.265021323850
7	1	159138663	ACB	0	190.600127463707
8	1	146364022	ACB	0	178.153765066457
9	1	141213431	ACB	0	180.473427901245
10	1	135534747	ACB	0	183.112946051943
11	1	135006516	ACB	0	161.856040732417
12	1	133851895	ACB	0	175.135319818982
13	1	115169878	ACB	0	129.792343512781
14	1	107349540	ACB	0	116.769337917254
15	1	102531392	ACB	0	150.840678460388
16	1	90354753	ACB	0	131.133808635308
17	1	81195210	ACB	0	128.534336575192
18	1	78077248	ACB	0	120.142569670562
19	1	59128983	ACB	0	106.857742811287
20	1	63025520	ACB	0	110.205396293913
21	1	48129895	ACB	0	64.651463886813
22	1	51304566	ACB	0	75.1198605516705
23	1	155270560	ACB	0	202.1689

In other words, as described in the tracts documentation, the file format should be as follows:

chrom	begin	end	assignment	cmBegin      cmEnd

I hope this helps!

P.S. Either you or Alicia has to close the issue :)