search

stat-lab / EvalSVcallers

Evaluate the performances (precision and recall) of structural variation (SV) callers
32 stars 13 forks source link

Parameters used for aligning short and long read data? #2

Closed joshuak94 closed 4 years ago

joshuak94 commented 4 years ago

Hello,

I'd like to use the scripts here to compare another structural variant caller, Vaquita. However, I would like to recreate the datasets as exactly as possible. I've downloaded the same short read sets (data1 to data4), but the paper only says that they were aligned with bwa. Am I right in assuming the following commands:

bwa aln hs37d5.fa ERR174336_1.fastq.gz > ERR174336_1.sai
bwa aln hs37d5.fa ERR174336_2.fastq.gz > ERR174336_2.sai
bwa sampe ERR174336_1.sai ERR174336_2.sai ERR174336_1.fastq.gz ERR174336_1.fastq.gz > ERR174336.sam
stat-lab commented 4 years ago

Dear Joshua,

I recommend to use the bwa men command as follows:

bwa mem [indexed reference fasta] [read_1.fastq.gz] [read_2.fastq.gz] -t -M > out.sam

Best,

Shunichi Kosugi

2019/09/05 20:09、Joshua Kim notifications@github.comのメール:

Hello,

I'd like to use the scripts here to compare another structural variant caller, Vaquita https://github.com/seqan/vaquita. However, I would like to recreate the datasets as exactly as possible. I've downloaded the same short read sets (data1 to data4), but the paper only says that they were aligned with bwa. Am I right in assuming the following commands:

bwa aln hs37d5.fa ERR174336_1.fastq.gz > ERR174336_1.sai bwa aln hs37d5.fa ERR174336_2.fastq.gz > ERR174336_2.sai bwa sampe ERR174336_1.sai ERR174336_2.sai ERR174336_1.fastq.gz ERR174336_1.fastq.gz > ERR174336.sam — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/stat-lab/EvalSVcallers/issues/2?email_source=notifications&email_token=ADIBV3AIEP6ARQOS7MHZQ2LQIDSG7A5CNFSM4IT4QVYKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HJP757A, or mute the thread https://github.com/notifications/unsubscribe-auth/ADIBV3AIUKBXZP4D5INXLE3QIDSG7ANCNFSM4IT4QVYA.

joshuak94 commented 4 years ago

Thank you! I realized I was using an older version of bwa which didn't have the mem command.

Could you quickly confirm the version used by your group?

stat-lab commented 4 years ago

The version of bwa we are using is 0.7.13.