使用samtools 1.10 發(fā)現(xiàn)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 參數
-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 用來call 普通二倍體 單樣品;-m 可以call 多樣品合并的bam ,發(fā)現(xiàn)一些稀有變異,應該就是 群call
