bcftools 替代samtools 产生vcf

使用samtools 1.10 发现不能生成vcf了

samtools mpileup

image.png

export PATH=/softwares/miniconda3/envs/mutation_detection/bin:$PATH
ref=path/02.bwa/reference/xxxxx.fasta
reads=xxx
bed=chr6-12.bed

for i in `ls path/04.bcftools_call/*bam ` ;do
sample=`basename ${i} | awk -F "." '{print $1 }'`
bcftools mpileup  \
    --regions-file ${bed} \
    --fasta-ref ${ref} \
    $i  \
| bcftools call \
   -cv \
   -o  ${sample}.bcftools.consensus-caller.raw.vcf 


#chr6-12.bed
#6  0   1124234324
#12 0   1123312223

bcftools call 中有 -c -m 参数

   -c, --consensus-caller          the original calling method (conflicts with -m)
   -m, --multiallelic-caller       alternative model for multiallelic and rare-variant calling (conflicts with -c)

理解是 -c 用来call 普通二倍体 单样品;-m 可以call 多样品合并的bam ,发现一些稀有变异,应该就是 群call

双等位基因(biallelic sites )和多等位基因(multiallelic sites)

参考:
bcftools进行SNP calling
Biallelic vs Multiallelic sites