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Old 02-19-2015, 01:49 PM   #1
SadiqAmin
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Location: Islamabad

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Default Generate a SAM file containing aligned reads GATK Error

Hello All,
I am a new bee here and entirely new to bioinformatics, I am working on the tutorial of GATK. I using its command to map and mark duplicates . Here these commands i am using
bwa mem -M -R "@RG\tID:group1\tSM:sample1\tPL:illumina\tLB:lib1\tPU:unit1" -p ucsc.hg19.fasta gcat_set_037_2.fastq > aligned_reads.sam

i am getting this error.
[bwt_restore_sa] fail to open file 'ucsc.hg19.fasta.sa' : No such file or directory


Please guide me what i am doing wrong.
regards
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Old 02-19-2015, 02:47 PM   #2
swbarnes2
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Is ucsc.hg19.fasta in that directory? Is it properly indexed?
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Old 02-19-2015, 04:14 PM   #3
SadiqAmin
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Yes its in the same folder, I am re indexing it again .
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bwa alignment, gatk alignment pipeline, sam

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