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mpileup2snp do not detect all snps #56

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wwang-chcn opened this issue Sep 25, 2020 · 0 comments
Open

mpileup2snp do not detect all snps #56

wwang-chcn opened this issue Sep 25, 2020 · 0 comments

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@wwang-chcn
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I have two samples names TL & TU. The coverage of bam looked like this.
Screen Shot 2020-09-25 at 11 01 01 AM
After running mpileup2snp using this command: samtools mpileup -B -f ~/source/bySpecies/danRer7/danRer7.fa TL_sorted.bam | java -jar ~/software/VarScan.v2.4.2.jar mpileup2snp - --min-freq-for-hom 1.0 > TL_varscan_output.txt
The output have few snps in this regions.
TL:
Screen Shot 2020-09-25 at 11 01 18 AM
TU:
Screen Shot 2020-09-25 at 11 01 30 AM
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