pileup: 产生基于位置的结果和 consensus/indel calling 3.最常用的三板斧就是格式转换,排序,索引 转换:samtools view -S SRR3589912.sam-b > SRR3589912.bam(-S是最新版的samtools为了兼容以前的版本写的) 排序:samtools sort SRR3589912.bam-o SRR3589912_sorted.bam 索引:samtools index SRR3589912_sorte...
Obviously this requires the MD and NM tags to be present, so adding them when they weren't there originally or removing them when they were there will change consensus unless the--no-adj-MQoption is given.
DP4 int[4] # high-quality reference forward bases, ref reverse, alternate for and alt rev bases FQ int Consensus quality. Positive: sample genotypes different; negative: otherwise MQ int Root-Mean-Square mapping quality of covering reads PC2 int[2] Phred probability of AF in group1 samples b...
DP4 int[4] # high-quality reference forward bases, ref reverse, alternate for and alt rev bases FQ int Consensus quality. Positive: sample genotypes different; negative: otherwise MQ int Root-Mean-Square mapping quality of covering reads PC2 int[2] Phred probability of AF in group1 samples b...
consensus.1.gz /usr/share/man/man1/samtools-coverage.1.gz /usr/share/man/man1/samtools-cram-size.1.gz /usr/share/man/man1/samtools-depad.1.gz /usr/share/man/man1/samtools-depth.1.gz /usr/share/man/man1/samtools-dict.1.gz /usr/share/man/man1/samtools-faidx.1.gz /usr/share/...
Add multi-threading to samtools consensus. Needs htslib#1875 Feb 14, 2025 .appveyor.yml Disable Appveyor build on all branches (#2108) Sep 5, 2024 .cirrus.yml Improve htslib#PRnum support for Cirrus-CI and GitHub Actions Sep 25, 2024 ...
2.AMTools的主要功能如下：view: BAM-SAM/SAM-BAM 转换和提取部分⽐对 sort: ⽐对排序 merge: 聚合多个排序⽐对 index: 索引排序⽐对 faidx: 建⽴FASTA索引，提取部分序列 tview: ⽂本格式查看序列 pileup: 产⽣基于位置的结果和 consensus/indel calling 3.最常⽤的三板斧就是格式转换，排序，...
Consensus/Variant Calling Options: -c Call variants using Bayesian inference. This option automatically invokes option -e. -d FLOAT When -v is in use, skip loci where the fraction of samples covered by reads is below FLOAT. [0] 当有多个sample用于variants calling时,比如多个转录组数据或多个重...
FQ int Consensus quality. Positive: sample genotypes different; negative: otherwise MQ int Root-Mean-Square mapping quality of covering reads PC2 int[2] Phred probability of AF in group1 samples being larger (,smaller) than in group2 PCHI2 double Posterior weighted chi^2 P-value between group...
Tag Format DescriptionAF1 double Max-likelihood estimate of the site allele frequency (AF) of the first ALT alleleDP int Raw read depth (without quality filtering)DP4 int[4] # high-quality reference forward bases, ref reverse, alternate for and alt rev basesFQ int Consensus quality. Positive:...