Picard SamToFastq strange behavious

reema · 02-27-2014, 02:59 AM

Dear all,

I am using picard SamtoFastq in oredr to convert BAM/SAM to fastq. I have a paired end sample. I am using following command:-

java -jar SamToFastq.jar INPUT=input.bam FASTQ=input_1.fastq SECOND_END_FASTQ=input_2.fastq VALIDATION_STRINGENCY=LENIENT

The command runs without error and generate two file. Now the problem is input_1.fastq has all the reads where as input_2.fastq is empty(o byte file). I have no idea why it's happening. I tried following option but no luck,
1) Sorted bam -> SamToFastq
2) BAM to SAM -> SamToFastq

Any suggestion would be very helpful.

Thanks,
Reema SIngh

TiborNagy · 02-27-2014, 06:32 AM

Maybe you BAM file is not a paired end sample. Check it manually.

reema · 03-05-2014, 07:27 AM

Quote:

Originally Posted by TiborNagy

Maybe you BAM file is not a paired end sample. Check it manually.

Thanks TiborNagy,

You are right,my file is not paired.

.

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02-27-2014, 02:59 AM	#1
reema Member Location: Scotland Join Date: Feb 2014 Posts: 27	Picard SamToFastq strange behavious Dear all, I am using picard SamtoFastq in oredr to convert BAM/SAM to fastq. I have a paired end sample. I am using following command:- java -jar SamToFastq.jar INPUT=input.bam FASTQ=input_1.fastq SECOND_END_FASTQ=input_2.fastq VALIDATION_STRINGENCY=LENIENT The command runs without error and generate two file. Now the problem is input_1.fastq has all the reads where as input_2.fastq is empty(o byte file). I have no idea why it's happening. I tried following option but no luck, 1) Sorted bam -> SamToFastq 2) BAM to SAM -> SamToFastq Any suggestion would be very helpful. Thanks, Reema SIngh

02-27-2014, 06:32 AM	#2
TiborNagy Senior Member Location: Budapest Join Date: Mar 2010 Posts: 329	Maybe you BAM file is not a paired end sample. Check it manually.