Entering edit mode
2.1 years ago
Sabeen
▴
30
Hi everyone, I am running a DNA seq analysis using FASTQ file. After running cutadapt for adapter removal and bwa for alignment i have got a bam file. Running the bam file through gatk ValidateSamFile gives me these two errors. MISMATCH_SEQ_QUAL_LENGTH and MISMATCH_READ_LENGTH_AND_QUALS_LENGTH. I would be thankful if someone can tell me how to fix these errors. Thanks.
Please show us all your commands and the outputs from all of them.
Hello Ram,
Thanks for reply.
This is all the commands I am using with the error msg at the end