...t alignment file
split splits a file by read group
quickcheck quickly check if SAM/BAM/CRAM file appears intact
fastq converts a BAM to a FASTQ
fasta converts a BAM to a FASTA
-- Statistics
bedcov read depth per BED region
depth...
...generated? (BLUE = best linear unbiased estimate) (Default: false)
-saveToFile <true | false> : Should the results be saved to a file rather than stored in memory? It true, the results will be written to a file as each SNP is analyzed in order to reduce memory requirementsand the results will...
...and line syntax is changing.
**********
********** For more information, please see:
**********
https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
**********
********** The command line looks like this in the new syntax:
**********
*****...
这是我的报错：
rm: cannot remove ‘/work/out/tmp_in/*’: No such file or directory
Options done
Output selected CAPS file name is: CAPS_output/selected_CAPS_primers.txt
ids is []
SNP_A, SNP_B G A
CAPS found with enzyme BstNI,PspGI,19
One nt can be changed to fit enzyme NlaIII...
我要做Gwas分析，需要生成hapmap文件，但是我直接用vcf转hapmap会报错Please first use SortGenotypeFilePlugin to correctly order the file.所以我就用tassel去排序然后可以正常生成hapmap文件了，但是我的两条比较小的contig不见了
...umn types or set `show_col_types = FALSE` to quiet this message.
Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
In addition: Warning message:
In file(file, "rt") :
cannot open file 'NA/pathway2name.tsv': No such file or directory
Execution halted
已经...
...fo for package tornado
Traceback (most recent call last):
File "<string>", line 17, in <module>
File "/tmp/pip_build_root/tornado/setup.py", line 146, in <module>
raise ImportError("Tornado requires an up-to-date SSL module. This means "
...