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Old 02-10-2016, 08:27 PM   #1
vaibhavvsk
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Location: Pune

Join Date: Sep 2011
Posts: 14
Question mpileup core dumped error with input fasta aligned bamfile.

I did bwa mem human alignment with single end fasta file. I tried running samtools mpileup & i'm getting same error as mentioned in thread as :Aborted (core dumped)
Command used was :
samtools mpileup -g -u -f /hg19/referenceFile/genome.fa MDS03_T_DRR001284_1111_small_fasta-quality_checked.bam > MDS03_T_DRR001284_1111_small_fasta-quality_checked__mpileup
There's no such exact error cause displayed on stdout.I tried solutions on https://www.biostars.org/p/132723/#176275
& I could get rid of this error using -R and -B options both independently. However there's difference between the variants obtained in vcf file after bcftools.
How to debug the exact cause and which fix to be used either -B or -R?
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