SARS-CoV-2-FASTA-freebayes 流程记录

zhanglu

地址：https://github.com/cfarkas/SARS-CoV-2-freebayes
其中参考序列为：https://github.com/cfarkas/SARS-CoV-2-freebayes/blob/master/CDC_HK_Pasteur_primers.fasta

测试命令

minimap2 -ax sr /ceph_disk1/xinguan/SARS-CoV-2-freebayes/covid19-refseq.fasta SRR11728611.fastp.gz > SRR11728611.sam 
minimap2 -ax sr /ceph_disk1/xinguan/SARS-CoV-2-freebayes/covid19-refseq.fasta SRR11728650.fastp.gz > SRR11728650.sam

samtools view -bS SRR11728611.sam > SRR11728611.bam
samtools view -bS SRR11728650.sam > SRR11728650.bam

samtools sort SRR11728611.sam  > SRR11728611.sorted.bam
samtools sort SRR11728650.sam  > SRR11728650.sorted.bam

samtools index SRR11728611.sorted.bam
samtools index SRR11728650.sorted.bam


freebayes -f /ceph_disk1/xinguan/SARS-CoV-2-freebayes/covid19-refseq.fasta -C 1 SRR11728611.sorted.bam > vcf/SRR11728611.freebayes.vcf
freebayes -f /ceph_disk1/xinguan/SARS-CoV-2-freebayes/covid19-refseq.fasta -C 1 SRR11728650.sorted.bam > vcf/SRR11728650.freebayes.vcf

jacquard merge --include_all ./vcf merged.vcf

问题一：参考序列格式不规范，在 jacquard merge --include_all ./vcf merged.vcf 会出错
（key error）
错误格式：

NC_045512.2 Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome
ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAA

修改为：

NC_045512.2 Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1
ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAA