bwa not generating sam file when provided with simulator's output

[mrpk123]

Hi,

I tried to simulate chr7.fa with 1000 random SNPs with the command

perl simuG.pl -refseq chr7.fa -snp_count 1000 -prefix simulated

Then I tried to generate sam file using bwa. Got following error

Would appreciate if you provide any pointers.

Please note, bwa worked very well with the original chr7.fa
Regards
Mrinal

[yjx1217]

Hi Mrinal,

Thanks for trying out simuG!
In its current implementation, simuG is for simulating the genome but not the reads, but you can simulate reads using read simulator (e.g. ART for Illumina reads) based on the simulated genome generated by simuG. You can check the supplementary note of our simuG paper for how to do this. After generating the simulated reads, you can map them back to the reference genome to call variants that were introduced by simuG. The supplementary note should also guide you to this point.

Please let me know if you have further questions.

Best,
Jia-Xing

[mrpk123]

Hi Jia-Xing, Got it. Thank you so much for your prompt reply. Regards Mrinal From: Jia-Xing Yue <notifications@github.com> Sent: Thursday, May 23, 2019 6:06 PM To: yjx1217/simuG <simuG@noreply.github.com> Cc: Mrinal Puranik <mrinal_puranik@persistent.com>; Author <author@noreply.github.com> Subject: Re: [yjx1217/simuG] bwa not generating sam file when provided with simulator's output (#1) Hi Mrinal, Thanks for trying out simuG! In its current implementation, simuG is for simulating the genome but not the reads, but you can simulate reads using read simulator (e.g. ART for Illumina reads) based on the simulated genome generated by simuG. You can check the supplementary note<https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/bioinformatics/PAP/10.1093_bioinformatics_btz424/1/btz424_supplementary_data.pdf?Expires=1558708370&Signature=eDbZ~XgewKxSMTQgIv-KX6~866bMqjmZWzos75HNh~oFBboz8qgKhvWUK11hTy9SxivRoBm3pjJNMFvpGELPpH11mChcjn7w3pkPc3X8~ChcM~1a7tZyXeH1ZImGJV6GVRCQAVId45yJCb7A41mQ3JjC-tZ6fXxdNEq4fiSFZ-lIEdI181r1cD8LMd8cQwVhswCFieDPg9i3Nte015moUXI0D25rsoKRmcQD6hRLJIKWGldWdkHp8b9uDJAKePZpP942qFty3v8fCamcnbN3H05~l1JVrf4UE6uyhcsgwmhIs6LjyCbsr18faXONKNP2p0IIosR4~jLKGtdVeoMpmQ__&Key-Pair-Id=APKAIE5G5CRDK6RD3PGA> of our simuG paper for how to do this. Please let me know if you have further questions. Best, Jia-Xing — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#1?email_source=notifications&email_token=AMEMJBIWXNUVU35S4UH7FM3PW2FTPA5CNFSM4HPBLODKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODWCCP6A#issuecomment-495200248>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AMEMJBJHYZSEUT5COLJX2LTPW2FTPANCNFSM4HPBLODA>. DISCLAIMER ========== This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails.

[yjx1217]

You are welcome! :-)
I am closing this issue now.

Best,
Jia-Xing