STAR aligner samtools mpileup C50

Question

[zeyuchen2016]

I use STAR align different RNA-SEQ sample to ref genome，then use samtools mpileup call snp

samtools mpileup -u -q 20 -Q 25 -C50 -b /public/home/zychen/staralignments/rmduplist --VCF --output-tags INFO/AD,AD,DP,SP -f /public/home/zychen/rna-seq/filterfq2085/rice_MC1314_genomes_v7.fasta |bcftools call --keep-alts  --multiallelic-caller  --variants-only -O v - > all_test.vcf

when I did'nt add -C50, MQ will become 20 at every site if I add -C50,MQ will different

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