[Samtools-help] samtools sort -n

[Rebecca H. <re...@gm...>]

Hi,

I have a couple of genomes, aligned to the same reference, that I am trying
to merge using the command:

java -jar picard.jar MergeSamFiles MERGE_SEQUENCE_DICTIONARIES=true
I=NA18867.bam I=Denisovan.bam O=out.bam

Upon merging, I get an error that my BAM files are in different orders - in
particular 2 and 19. So, I attempted to use samtools sort -n to sort all my
BAM files. However, this is not working as expected. After sorting, I used
samtools view -H to look at the header of my sorted BAM files (results
shown below) and find that these genomes continue to be in different orders.

I am using samtools version 1.2 and the following command for sorting:
samtools sort -n -T human -o humans/NA18867.sorted.bam -O bam -@ 12
humans/NA18867.bam

Any help would be greatly appreciated. Thanks!
Rebecca


For one genome I get:

@HD VN:1.0 SO:queryname

@SQ SN:1 LN:249250621

@SQ SN:10 LN:135534747

@SQ SN:11 LN:135006516

@SQ SN:12 LN:133851895

@SQ SN:13 LN:115169878

@SQ SN:14 LN:107349540

@SQ SN:15 LN:102531392

@SQ SN:16 LN:90354753

@SQ SN:17 LN:81195210

@SQ SN:18 LN:78077248

@SQ SN:19 LN:59128983
@SQ SN:2 LN:243199373

and for the other genome I get:

@HD VN:1.0 GO:none SO:queryname

@SQ SN:1 LN:249250621 AS:NCBI37 UR:
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz
M5:1b22b98cdeb4a9304cb5d48026a85128 SP:Human

@SQ SN:2 LN:243199373 AS:NCBI37 UR:
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz
M5:a0d9851da00400dec1098a9255ac712e SP:Human

@SQ SN:3 LN:198022430 AS:NCBI37 UR:
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz
M5:fdfd811849cc2fadebc929bb925902e5 SP:Human

@SQ SN:4 LN:191154276 AS:NCBI37 UR:
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz
M5:23dccd106897542ad87d2765d28a19a1 SP:Human