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  • extract fast from bam taking SV into account

    Hi,
    I have a bam file that includes a big indel and a translocation. I wish to extract a new reference fasta file with the SV (without the deleted region and with the translocation). I also preform a de novo assembly so I want to compare the two outputs I got. What is the wright way to do so?


    I tried:
    Code:
    samtools mpileup -uf ref.fa test.bam | bcftools call -c | vcfutils.pl vcf2fq > test.fastq
    I do not think it includes the SVs inside. Any suggestions?

    Thanks
    Last edited by EHC; 03-16-2022, 01:10 AM.

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