I have a BAM file generated from single-end data and I want to estimate the insert size using picard's CollectInsertSizeMetrics
as follows:
java -jar Picard/picard.jar CollectInsertSizeMetrics I=Ctrl_sorted.bam O=Ctrl.insert_sizes.txt H=Ctrl.insert_sizes.pdf M=0.5 MAX_RECORDS_IN_RAM=2000000 VALIDATION_STRINGENCY=LENIENT
It runs fine until at the very end I get the following message:
WARNING 2023-01-31 15:37:13 CollectInsertSizeMetrics All data categories were discarded because they contained < 0.5 of the total aligned paired data.
Picard obviously thinks the data should be paired-end, so is there a way to tell it that it is single-end? I cannot find an option for this:
java -jar picard.jar CollectInsertSizeMetrics -h
USAGE: CollectInsertSizeMetrics [arguments]
Collect metrics about the insert size distribution of a paired-end library. This tool provides useful metrics for
validating library construction including the insert size distribution and read orientation of paired-end
libraries.</p>The expected proportions of these metrics vary depending on the type of library preparation used,
resulting from technical differences between pair-end libraries and mate-pair libraries. For a brief primer on
paired-end sequencing and mate-pair reads, see the <a
href='https://www.broadinstitute.org/gatk/guide/article?id=6327'>GATK Dictionary</a>.<p>The CollectInsertSizeMetrics
tool outputs the percentages of read pairs in each of the three orientations (FR, RF, and TANDEM) as a histogram. In
addition, the insert size distribution is output as both a histogram (.insert_size_Histogram.pdf) and as a data table
(.insert_size_metrics.txt).</p><p>Note: Metrics labeled as percentages are actually expressed as fractions!</p><h4>Usage
example:</h4><pre>java -jar picard.jar CollectInsertSizeMetrics \<br /> I=input.bam \<br />
O=insert_size_metrics.txt \<br /> H=insert_size_histogram.pdf \<br /> M=0.5</pre>Note: If processing a small
file, set the minimum percentage option (M) to 0.5, otherwise an error may occur. <br /><br />Please see <a
href='https://broadinstitute.github.io/picard/picard-metric-definitions.html#InsertSizeMetrics'>InsertSizeMetrics</a>
for detailed explanations of each metric.<hr />
Version:2.23.8
Required Arguments:
--Histogram_FILE,-H:File File to write insert size Histogram chart to. Required.
--INPUT,-I:File Input SAM or BAM file. Required.
--OUTPUT,-O:File The file to write the output to. Required.
Optional Arguments:
--arguments_file:File read one or more arguments files and add them to the command line This argument may be
specified 0 or more times. Default value: null.
--ASSUME_SORTED,-AS:Boolean If true (default), then the sort order in the header file will be ignored. Default value:
true. Possible values: {true, false}
--COMPRESSION_LEVEL:Integer Compression level for all compressed files created (e.g. BAM and VCF). Default value: 5.
--CREATE_INDEX:Boolean Whether to create an index when writing VCF or coordinate sorted BAM output. Default
value: false. Possible values: {true, false}
--CREATE_MD5_FILE:Boolean Whether to create an MD5 digest for any BAM or FASTQ files created. Default value:
false. Possible values: {true, false}
--DEVIATIONS:Double Generate mean, sd and plots by trimming the data down to MEDIAN +
DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION. This is done because insert size data typically
includes enough anomalous values from chimeras and other artifacts to make the mean and sd
grossly misleading regarding the real distribution. Default value: 10.0.
--GA4GH_CLIENT_SECRETS:String Google Genomics API client_secrets.json file path. Default value: client_secrets.json.
--help,-h:Boolean display the help message Default value: false. Possible values: {true, false}
--HISTOGRAM_WIDTH,-W:Integer Explicitly sets the Histogram width, overriding automatic truncation of Histogram tail.
Also, when calculating mean and standard deviation, only bins <= Histogram_WIDTH will be
included. Default value: null.
--INCLUDE_DUPLICATES:Boolean If true, also include reads marked as duplicates in the insert size histogram. Default
value: false. Possible values: {true, false}
--MAX_RECORDS_IN_RAM:Integer When writing files that need to be sorted, this will specify the number of records stored
in RAM before spilling to disk. Increasing this number reduces the number of file handles
needed to sort the file, and increases the amount of RAM needed. Default value: 500000.
--METRIC_ACCUMULATION_LEVEL,-LEVEL:MetricAccumulationLevel
The level(s) at which to accumulate metrics. This argument may be specified 0 or more
times. Default value: [ALL_READS]. Possible values: {ALL_READS, SAMPLE, LIBRARY,
READ_GROUP}
--MIN_HISTOGRAM_WIDTH,-MW:Integer
Minimum width of histogram plots. In the case when the histogram would otherwise
betruncated to a shorter range of sizes, the MIN_HISTOGRAM_WIDTH will enforce a minimum
range. Default value: null.
--MINIMUM_PCT,-M:Float When generating the Histogram, discard any data categories (out of FR, TANDEM, RF) that
have fewer than this percentage of overall reads. (Range: 0 to 1). Default value: 0.05.
--QUIET:Boolean Whether to suppress job-summary info on System.err. Default value: false. Possible
values: {true, false}
--REFERENCE_SEQUENCE,-R:File Reference sequence file. Default value: null.
--STOP_AFTER:Long Stop after processing N reads, mainly for debugging. Default value: 0.
--TMP_DIR:File One or more directories with space available to be used by this program for temporary
storage of working files This argument may be specified 0 or more times. Default value:
null.
--USE_JDK_DEFLATER,-use_jdk_deflater:Boolean
Use the JDK Deflater instead of the Intel Deflater for writing compressed output Default
value: false. Possible values: {true, false}
--USE_JDK_INFLATER,-use_jdk_inflater:Boolean
Use the JDK Inflater instead of the Intel Inflater for reading compressed input Default
value: false. Possible values: {true, false}
--VALIDATION_STRINGENCY:ValidationStringency
Validation stringency for all SAM files read by this program. Setting stringency to
SILENT can improve performance when processing a BAM file in which variable-length data
(read, qualities, tags) do not otherwise need to be decoded. Default value: STRICT.
Possible values: {STRICT, LENIENT, SILENT}
--VERBOSITY:LogLevel Control verbosity of logging. Default value: INFO. Possible values: {ERROR, WARNING,
INFO, DEBUG}
--version:Boolean display the version number for this tool Default value: false. Possible values: {true,
false}
Advanced Arguments:
--showHidden,-showHidden:Boolean
display hidden arguments Default value: false. Possible values: {true, false}
Or is there another tool that can deal with single-end data to estimate the insert size?