varscan can't call a SNV

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2.8 years ago

tan ▴ 10

i can see a mutation in my bam file by IGV，but，when i use varscan to call it，i can't find enter image description here my cmd

samtools mpileup  -Q 20 -C 50 -q 20 -d 20000 -f ucsc.hg19.fasta  -l test.bed   bam/test.bam  >varscan/test.dedup.mpileup
java -jarVarScan.v2.3.9.jar   mpileup2snp  varscan/test.dedup.mpileup  --min-coverage 4 --min-reads2 2 --min-avg-qual 20 --min-var-freq 0.001 --min-freq-for-hom 0.9 --output-vcf 1 >varscan/test_snp.vcf

i have checked test.dedup.mpileup

grep chr17  varscan/test.dedup.mpileup|grep 37879657

enter image description here I'm confused why varscan no call it？ or Is there any way to enter debug mode ？

any suggestions on ctDNA analysis are also appreciated，Thanks in advance，

varscan igv • 860 views

ADD COMMENT • link 2.8 years ago by tan ▴ 10

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--min-coverage 4? Or any other heuristic that kicks in here?

ADD REPLY • link 2.8 years ago by ATpoint 85k

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I tried many possibilities，even adjusted the threshold of p to a large value，I think that when there is more than one mutation in a pos, the software will not call it enter image description here out，it I encountered a similar situation again

ADD REPLY • link 2.8 years ago by tan ▴ 10

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