Changes between Version 39 and Version 40 of SOPs/miningSAMBAM


Ignore:
Timestamp:
12/05/17 10:17:53 (7 years ago)
Author:
gbell
Comment:

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  • SOPs/miningSAMBAM

    v39 v40  
    181181bsub "samtools view -b -F 0x0040 accepted_hits.bam > accepted_hits_2ndPair.bam"
    182182}}}
     183
     184=== Print consensus sequence of mapped reads ===
     185{{{
     186samtools mpileup -uf ref_genome.fa Mapped_reads.bam >| Mapped_reads.variants.bcf
     187bcftools call -O v -c Mapped_reads.variants.bcf | vcfutils.pl vcf2fq -d 2 >| Mapped_reads.consensus.fq
     188}}}