Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

picard.PicardException: Input paired fastq files must be the same length

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    Bhanu Gandham

    Can you confirm that both the forward and reverse fastqs have equal number of reads?

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    Keren

    Hi Bhanu,  I realized that for those failed samples. The forward and reverse fastqs are of different lengths. Should I convert them to equal number of reads before feeding them to fastqtosam? Do you know any way that I can filter them to same length?   Many thanks!!  

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    danilovkiri

    Hi Keren

    It is imperative for paired-end FASTQ data to have the same amount of reads. Besides, the order of the reads in R1 file must correspond to the order in R2 file. I suggest you try to retrieve your FASTQ data form the source and find out what preprocessing steps resulting in FASTQ malformation have been taken prior to FastqToSam. There is no correct way to restore the data. The only option (except the one mentioned above) is to use tools which discard unpaired reads (singletons) from FASTQ. I suggest you try this one https://github.com/linsalrob/fastq-pair. If it does not work, ask somebody to help you install it. The least favourable options are mentioned here https://www.biostars.org/p/56171/

     

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    Keren

    Thank you! This is very helpful. I will try out the fastq-pair package. 

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    Bhanu Gandham

    I agree with Keren this is indeed very helpful information! Thank you danilovkiri!! 

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