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Results tagged with samtools
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user 35
Questions specific to interacting with and post-processing sequence alignments using the SAMtools package. For questions specifically about formats SAM, BAM or CRAM use tags sam or bam,
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variant calling on ChIP-seq style data: samtools mpileup with minimal filters
I used this in the past for ChIP-seq data and it generated SNVs:
samtools mpileup \
--uncompressed --max-depth 10000 --min-MQ 20 --ignore-RG --skip-indels \
--fasta-ref ref.fa file.bam \
| bcftools call … --consensus-caller \
> out.vcf
This was samtools 1.3 in case that makes a difference. …
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