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verifyBamID checks whether reads in a BAM file match previous genotypes for a specific sample. However, since development occurs only on Ubuntu (9.10-13.10) x86 and 圆4 platforms, and later, there are likely other portability issues.Ī key step in any genetic analysis is to verify whether data being generated matches expectations. VerifyBamID is designed to be reasonably portable. LIB_PATH_VERIFY_BAM_ID = /path/to/libStatGen Replace: LIB_PATH_VERIFY_BAM_ID ?= $(LIB_PATH_GENERAL) with

Bam mailist list remove update#

If the libStatGen you want to use is at a different location then update verifyBamID's Makefile.inc. If you have a different version of libStatGen at that path, then skip the cloneLib step. libStatGen under your verifyBamID directory, and make will create binary of verifyBamID under verifyBamID/bin/ Note that make cloneLib command will create a directory.

Bam mailist list remove download#

If you download the source without libStatGen: If you download the source that includes libStatGen: You may use that version in Ubuntu 64-bit platform. The binary download of verifyBamID is available.

Estimated reference-bias parameters (useful mostly for ABI SOLiD sequence data).

Generate the depth distribution statistics.

Uses Brent's method for precise estimation of contamination parameters.

The reference sequence information is no longer required.

The genotype / allele frequency file is now based on VCF format rather than PLINK format.

(8) The new release of verifyBamID have undergone major change since the last version (as of 2011 April).

Changes in the directory structure and Makefile.

If your sequence data has very short insert size, this update may increase the sensitivity of estimated contamination. This option is turned on by default, and can be turned off usig -ignoreOverlapPair.

(IMPORTANT) Add an option to remove either side of overlapping fragment.

Fixed a bug of incorrect per-readgroup output (Thanks to Matthew Flickinger).

Fixed a bug of incorrect per-readgroup output in -chip-* parameter.

Fixed a bug of incorrect estimate of contamination when -chip-full option was used (Thanks to Richard Smith).

Added PhoneHome/Version Checking to VerifyBamID.

Please join in the VerifyBamID Google Group to ask / discuss / comment about verifyBamID. To get a copy of older releases go to the VerifyBamID Download download page.

You will need to download libStatGen separately if you do not already have it.

Bam mailist list remove code#

Source code (tar.gz) or Source code (zip).Source Code without libStatGen (allows alternative/newer versions of libStatGen).Cd into the resulting directory & type make. Souce Code including libStatGen (uses a fixed version of libStatGen).In other platforms, please download the source distribution and build it. Binary expected to run in Ubuntu 圆4 platform.Select the latest release and download in one of 3 ways: 9.3 A guideline to interpret output files.9.2 Column information in the output files.