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DiltheyLab / HLA-LA

Fast HLA type inference from whole-genome data
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Issue with bowtie2 #23

Closed valentinShimansky closed 5 years ago

valentinShimansky commented 5 years ago

Hello!

Excuse me for possible English mistakes. I've got an issue trying to make HLA typing with HLA-LA on NGS samples, which were aligned to hg38 reference using bowtie2, and HLA-LA gives me following mistake

Have found no compatible reference specifications in somepathonserver/HLA-PRG-LA/src/../graphs/PRG_MHC_GRCh38_withIMGT/knownReferences - create a file for this BAM file and try again. at somepathonserver/HLA-PRG-LA/src/HLA-PRG-LA.pl line 267.

And if I perform HLA typing with HLA-LA on the same samples, which were aligned to the same reference using BWA and it always works correct. Is there any known solution for this problem? I changed chromosome naming from 1 2 3 etc which is used by bowtie2 to chr1 chr2 chr3 used by BWA with samtools reheader but that didn't work out.

AlexanderDilthey commented 5 years ago

Hi,

HLA*LA uses the 'samtools idxstats' to figure out which reference it should use - is the output you get when you apply this command to your BWA- / bowtie2-based BAMs exactly identical?

Von: valentinShimansky notifications@github.com Gesendet: Montag, 20. Mai 2019 16:20 An: DiltheyLab/HLA-LA Cc: Subscribed Betreff: [DiltheyLab/HLA-LA] Issue with bowtie2 (#23)

Hello!

Excuse me for possible English mistakes. I've got an issue trying to make HLA typing with HLA-LA on NGS samples, which were aligned to hg38 reference using bowtie2, and HLA-LA gives me following mistake

Have found no compatible reference specifications in somepathonserver/HLA-PRG-LA/src/../graphs/PRG_MHC_GRCh38_withIMGT/knownReferences - create a file for this BAM file and try again. at somepathonserver/HLA-PRG-LA/src/HLA-PRG-LA.pl line 267.

And if I perform HLA typing with HLA-LA on the same samples, which were aligned to the same reference using BWA and it always works correct. Is there any known solution for this problem? I changed chromosome naming from 1 2 3 etc which is used by bowtie2 to chr1 chr2 chr3 used by BWA with samtools reheader but that didn't work out.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/DiltheyLab/HLA-LA/issues/23?email_source=notifications&email_token=ABQWY2KMNRYYNQVYPYOLGD3PWKXR3A5CNFSM4HOCOROKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4GUXUBZA, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ABQWY2J62YD3W5ZZCLECQSDPWKXR3ANCNFSM4HOCOROA.

valentinShimansky commented 5 years ago

Thank you for your quick response! Indeed, the problem is that the bam file we have was created by read alignment to human reference b38 without alternative contigs (as bowtie2 doesn't support them). The HLA-LA graphs only have a b38 reference with alternative contigs - and this causes the problem. Do you maybe already have a pre-computed graph for b38 only with chromosomes 1-22, X, Y, MT?

AlexanderDilthey commented 5 years ago

We support a variety of B38 references, but probably not this specific one - if you send me the output from 'samtools idxstats', I will create a suitable read extraction file.

Von: valentinShimansky notifications@github.com Gesendet: Dienstag, 21. Mai 2019 11:33 An: DiltheyLab/HLA-LA Cc: Alexander Dilthey; Comment Betreff: Re: [DiltheyLab/HLA-LA] Issue with bowtie2 (#23)

Thank you for your quick response! Indeed, the problem is that the bam file we have was created by read alignment to human reference b38 without alternative contigs (as bowtie2 doesn't support them). The HLA-LA graphs only have a b38 reference with alternative contigs - and this causes the problem. Do you maybe already have a pre-computed graph for b38 only with chromosomes 1-22, X, Y, MT?

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/DiltheyLab/HLA-LA/issues/23?email_source=notifications&email_token=ABQWY2NAIHRBGMCHXVVVW4DPWO6YBA5CNFSM4HOCOROKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODV3KV5Y#issuecomment-494316279, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ABQWY2J5ZIWXUP54UTJCXJDPWO6YBANCNFSM4HOCOROA.

valentinShimansky commented 5 years ago

thank you very much for fast support!! here is a result of idxstats

$ samtools idxstats /mnt/bakeoff/bakeoff/macrogen/bam/JH-016P/JH-016P.sorted.bam

Y 57227415 5949112 212376

X 156040895 22183702 122978

MT 16569 292952 2419

9 138394717 34693132 222424

8 145138636 40989813 224381

7 159345973 44649005 301559

6 170805979 48052957 245866

5 181538259 52302854 671007

4 190214555 55251440 553314

3 198295559 57555421 595000

22 50818468 12180645 198047

21 46709983 15577404 325147

20 64444167 19386056 254639

2 242193529 68184771 394031

19 58617616 16667535 283305

18 80373285 23107558 255262

17 83257441 23230709 227320

16 90338345 25482001 318546

15 101991189 23876948 149098

14 107043718 25432804 148130

13 114364328 27797080 194267

12 133275309 37682032 263946

11 135086622 37915067 211630

10 133797422 38379963 367438

1 248956422 67963304 564611

We support a variety of B38 references, but probably not this specific one - if you send me the output from 'samtools idxstats', I will create a suitable read extraction file. … ____ Von: valentinShimansky notifications@github.com Gesendet: Dienstag, 21. Mai 2019 11:33 An: DiltheyLab/HLA-LA Cc: Alexander Dilthey; Comment Betreff: Re: [DiltheyLab/HLA-LA] Issue with bowtie2 (#23) Thank you for your quick response! Indeed, the problem is that the bam file we have was created by read alignment to human reference b38 without alternative contigs (as bowtie2 doesn't support them). The HLA-LA graphs only have a b38 reference with alternative contigs - and this causes the problem. Do you maybe already have a pre-computed graph for b38 only with chromosomes 1-22, X, Y, MT? — You are receiving this because you commented. Reply to this email directly, view it on GitHub<#23?email_source=notifications&email_token=ABQWY2NAIHRBGMCHXVVVW4DPWO6YBA5CNFSM4HOCOROKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODV3KV5Y#issuecomment-494316279>, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ABQWY2J5ZIWXUP54UTJCXJDPWO6YBANCNFSM4HOCOROA.

AlexanderDilthey commented 5 years ago

Hi Valentin,

If you do a 'git pull' in your directory, it should download a read extraction file that is compatible with your reference. Please let me know if this doesn't work.

Best wishes,

Alexander

Von: valentinShimansky notifications@github.com Gesendet: Dienstag, 21. Mai 2019 13:49 An: DiltheyLab/HLA-LA Cc: Alexander Dilthey; Comment Betreff: Re: [DiltheyLab/HLA-LA] Issue with bowtie2 (#23)

thank you very much for fast support!! here is a result of idxstats

$ samtools idxstats /mnt/bakeoff/bakeoff/macrogen/bam/JH-016P/JH-016P.sorted.bam

Y 57227415 5949112 212376

X 156040895 22183702 122978

MT 16569 292952 2419

9 138394717 34693132 222424

8 145138636 40989813 224381

7 159345973 44649005 301559

6 170805979 48052957 245866

5 181538259 52302854 671007

4 190214555 55251440 553314

3 198295559 57555421 595000

22 50818468 12180645 198047

21 46709983 15577404 325147

20 64444167 19386056 254639

2 242193529 68184771 394031

19 58617616 16667535 283305

18 80373285 23107558 255262

17 83257441 23230709 227320

16 90338345 25482001 318546

15 101991189 23876948 149098

14 107043718 25432804 148130

13 114364328 27797080 194267

12 133275309 37682032 263946

11 135086622 37915067 211630

10 133797422 38379963 367438

1 248956422 67963304 564611

We support a variety of B38 references, but probably not this specific one - if you send me the output from 'samtools idxstats', I will create a suitable read extraction file. … ____ Von: valentinShimansky notifications@github.commailto:notifications@github.com Gesendet: Dienstag, 21. Mai 2019 11:33 An: DiltheyLab/HLA-LA Cc: Alexander Dilthey; Comment Betreff: Re: [DiltheyLab/HLA-LA] Issue with bowtie2 (#23https://github.com/DiltheyLab/HLA-LA/issues/23) Thank you for your quick response! Indeed, the problem is that the bam file we have was created by read alignment to human reference b38 without alternative contigs (as bowtie2 doesn't support them). The HLA-LA graphs only have a b38 reference with alternative contigs - and this causes the problem. Do you maybe already have a pre-computed graph for b38 only with chromosomes 1-22, X, Y, MT? — You are receiving this because you commented. Reply to this email directly, view it on GitHub<#23https://github.com/DiltheyLab/HLA-LA/issues/23?email_source=notifications&email_token=ABQWY2NAIHRBGMCHXVVVW4DPWO6YBA5CNFSM4HOCOROKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODV3KV5Y#issuecomment-494316279>, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ABQWY2J5ZIWXUP54UTJCXJDPWO6YBANCNFSM4HOCOROA.

thank you very much for fast responding!! here is a result of idxstats

$ samtools idxstats /mnt/bakeoff/bakeoff/macrogen/bam/JH-016P/JH-016P.sorted.bam

Y 57227415 5949112 212376

X 156040895 22183702 122978

MT 16569 292952 2419

9 138394717 34693132 222424

8 145138636 40989813 224381

7 159345973 44649005 301559

6 170805979 48052957 245866

5 181538259 52302854 671007

4 190214555 55251440 553314

3 198295559 57555421 595000

22 50818468 12180645 198047

21 46709983 15577404 325147

20 64444167 19386056 254639

2 242193529 68184771 394031

19 58617616 16667535 283305

18 80373285 23107558 255262

17 83257441 23230709 227320

16 90338345 25482001 318546

15 101991189 23876948 149098

14 107043718 25432804 148130

13 114364328 27797080 194267

12 133275309 37682032 263946

11 135086622 37915067 211630

10 133797422 38379963 367438

1 248956422 67963304 564611

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/DiltheyLab/HLA-LA/issues/23?email_source=notifications&email_token=ABQWY2N3QJH4ICCM4PJILCLPWPOVFA5CNFSM4HOCOROKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODV3U2EA#issuecomment-494357776, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ABQWY2ODKZPNBR3PCJXLG4LPWPOVFANCNFSM4HOCOROA.