does sort order matter?

[r corbett]

Hi. I'm following the instructions I found here to try and run
joinSNVMix. I am first running the "train" routine of a pair of 30X
tumour, normal genomes.

My command:
jsm.py train joint_snv_mix_two human.fasta normal tumour
joint_priors.cfg joint_params.cfg output.cfg
Randomly sub-sampling every 100th position with normal depth 10 and
tumour depth 10 the data set.
Subsampling ref 20.
Sub-sampled 577197 positions from ref 20
Subsampling ref 21.
Sub-sampled 331998 positions from ref 21
Subsampling ref 22.
Sub-sampled 331205 positions from ref 22
Subsampling ref 1.

I just wanted to confirm that the natural sort order assigned by
samtools will work here. Here is the Chr order I have:

@SQ SN:1 LN:247249719
@SQ SN:10 LN:135374737
@SQ SN:11 LN:134452384
@SQ SN:12 LN:132349534
@SQ SN:13 LN:114142980
@SQ SN:14 LN:106368585
@SQ SN:15 LN:100338915
@SQ SN:16 LN:88827254
@SQ SN:17 LN:78774742
@SQ SN:18 LN:76117153
@SQ SN:19 LN:63811651
@SQ SN:2 LN:242951149
@SQ SN:20 LN:62435964
@SQ SN:21 LN:46944323
@SQ SN:22 LN:49691432
@SQ SN:3 LN:199501827
@SQ SN:4 LN:191273063
@SQ SN:5 LN:180857866
@SQ SN:6 LN:170899992
@SQ SN:7 LN:158821424
@SQ SN:8 LN:146274826
@SQ SN:9 LN:140273252
@SQ SN:MT LN:16571
@SQ SN:X LN:154913754
@SQ SN:Y LN:57772954

[aroth]

The sort order should not matter, and could even be different in the
tumour and normal. The program fetches the read data by chromosome
name, so position in the BAM file (sort order) should have no effect.

Cheers,
Andy