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02-19-2015, 01:49 PM
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#1 |
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Junior Member
Location: Islamabad Join Date: Feb 2015
Posts: 2
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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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02-19-2015, 02:47 PM
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#2 |
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Senior Member
Location: San Diego Join Date: May 2008
Posts: 912
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Is ucsc.hg19.fasta in that directory? Is it properly indexed?
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02-19-2015, 04:14 PM
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#3 |
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Junior Member
Location: Islamabad Join Date: Feb 2015
Posts: 2
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Yes its in the same folder, I am re indexing it again .
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| Tags |
| bwa alignment, gatk alignment pipeline, sam |
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