how to modify sam file sort order

Question

[i19870503]

I got the error when I run cuffdiff

Error: sort order of reads in BAMs must be the same

so I use samtools view find that in this bam file, the others are sorted as chr1,chr2....not like this one.

How to modify the order to make it as other file?

@HD    VN:1.0    SO:coordinate
@SQ    SN:chr10    LN:66736929    UR:file:/home/group1/corona/ucsc2.fa    M5:171e7a3f72ba195f457720406be3604b
@SQ    SN:chr11    LN:79814395    UR:file:/home/group1/corona/ucsc2.fa    M5:feeab3090c18a3cab9547f99d35052a8
@SQ    SN:chr12    LN:57431344    UR:file:/home/group1/corona/ucsc2.fa    M5:f3309f09ea225f9a191b5d0d9eee961d
@SQ    SN:chr13    LN:145235301    UR:file:/home/group1/corona/ucsc2.fa    M5:3a4b8ac5120541c225eb870fa4a2b501
@SQ    SN:chr14    LN:148510138    UR:file:/home/group1/corona/ucsc2.fa    M5:c607e774abadba7ed0b0185f18e3f9d5
@SQ    SN:chr15    LN:134541103    UR:file:/home/group1/corona/ucsc2.fa    M5:08f26a29f88b39bff614cd6fbfa7d2ef
@SQ    SN:chr16    LN:77435658    UR:file:/home/group1/corona/ucsc2.fa    M5:0f5873a922aa3327b4523def56cad5e6
@SQ    SN:chr17    LN:64395339    UR:file:/home/group1/corona/ucsc2.fa    M5:ac533e777ca34fe996fdf58598266b98
@SQ    SN:chr18    LN:54309914    UR:file:/home/group1/corona/ucsc2.fa    M5:1cc33aec4862e0d56e691e5dc5960501
@SQ    SN:chr1    LN:295529705    UR:file:/home/group1/corona/ucsc2.fa    M5:2cf1f3b70031dc473022a5a5893e8edb
@SQ    SN:chr2    LN:140133492    UR:file:/home/group1/corona/ucsc2.fa    M5:b709bf0683d1abdca4f6236a45524577
@SQ    SN:chr3    LN:123599780    UR:file:/home/group1/corona/ucsc2.fa    M5:2e896d4cc99e908405eb690a71467e37
@SQ    SN:chr4    LN:136254946    UR:file:/home/group1/corona/ucsc2.fa    M5:32ceede4917f4ea64a7ab93040211d21
@SQ    SN:chr5    LN:100516970    UR:file:/home/group1/corona/ucsc2.fa    M5:50bd953e6de61fb729390a122f830653
@SQ    SN:chr6    LN:123305171    UR:file:/home/group1/corona/ucsc2.fa    M5:2ed43939ee3490a30cbe40e96cf33289
@SQ    SN:chr7    LN:136409062    UR:file:/home/group1/corona/ucsc2.fa    M5:57ed74ddd703b537d8fece561887bcf4
@SQ    SN:chr8    LN:119985671    UR:file:/home/group1/corona/ucsc2.fa    M5:deadaedc161e58bf8c8d6b3ea1c25eba
@SQ    SN:chr9    LN:132468591    UR:file:/home/group1/corona/ucsc2.fa    M5:89eae5d26c774408170957bb006efbbd
@SQ    SN:chrM    LN:16770    UR:file:/home/group1/corona/ucsc2.fa    M5:c32d2133c7327cc9e47776c5eed17977
@SQ    SN:chrX    LN:125871292    UR:file:/home/group1/corona/ucsc2.fa    M5:d09f454e7e0e413bdd5e65af386c581d
@RG    ID:20121127154622665    LB:50F    SM:1CM

Answer 1

[Ashutosh Pandey]

If you have a reference fasta file that contains chromosomes in your order of interest (i.e. chr1, chr2, ...) , you can use Picard's ReorderSam tools to sort your bam file. You will have to generate .dict file for your reference genome. Please go to https://broadinstitute.github.io/picard/command-line-overview.html and Ctrl+F for ReorderSam.

[i19870503]

Ok, got it. Thanks very much.

[i19870503]

One more question, if I convert the bam file to sam, could I modfiy the order munually.

[Ashutosh Pandey]

Yes, SAM is a tab delimited text file. You should be able to process it but I am not sure what would be your approach.