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  • 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?
    Vaibhav Kulkarni

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